PDB ID 1XC5: Solution Structure of the SMRT Deacetylase Activation Domain
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2D Diagram
2D Cartoon
Dynamically generated for selected residues. Nodes can be dragged or clicked.
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Dynamically Calculated Symmetry using SymD
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Select on 1D sequences: drag to select, drag again to deselect, multiple selection is allowed without Ctrl key, click "Save Selection" to save the current selection.
Select on 2D interaction diagram: click on the nodes or lines. The nodes are chains and can be united with the Ctrl key. The lines are interactions and can NOT be united. Each click on the lines selects half of the lines, i.e., select the interacting residues in one of the two chains.
Select on 3D structures: hold "Alt" and use mouse to pick, click the second time to deselect, hold "Ctrl" to union selection, hold "Shift" to select a range, press the up/down arrow to switch among atom/residue/strand/chain/structure, click "Save Selection" to save the current selection.
Save the current selection(either on 3D structure, 2D interactions, or 1D sequence): open the menu "Select -> Save Selection", specify the name and description for the selection, and click "Save".
Residue labeling: aligned residue with coordinates: UPPER case letter; non-aligned residue with coordinates: lower case letter which can be highlighted; residue missing coordinates: lower case letter which can NOT be highlighted.
Select Residues in Aligned Sequences
Defined Sets
Defined Sets: Set Operations:
Select:
Name:
Specification Tips:
Specification: In the selection "$1HHO,4N7N.A,B,C:5-10,LV,3AlaVal,chemicals@CA,C,C*":
"$1HHO,4N7N" uses "$" to indicate structure selection.
".A,B,C" uses "." to indicate chain selection.
":5-10,LV,3LeuVal,chemicals" uses the colon ":" to indicate residue selection. Residue selection could be residue number(5-10), one-letter IUPAC residue name abbreviations(LV), three-letter residue names(AlaVal, "3" indicates each residue name has three letters), or predefined names: "proteins", "nucleotides", "chemicals", "ions", and "water". IUPAC abbreviations can be written either as a contiguous string(e.g., ":LV"), in order to find all instances of that sequence in the structure, or they can be separated by commas(e.g., ":L,V") to select all residues of a given type in the structure(in the latter case, select all Leucine and Valine in the structure).
"@CA,C,C*" uses "@" to indicate atom name selection. "C*" selects any atom names starting with "C".
Partial definition is allowed, e.g., ":1-10" selects all residue IDs 1-10 in all chains.
Different selections can be unioned(with "or", default), intersected(with "and"), or negated(with "not"). For example, ":1-10 or :K" selects all residues 1-10 and all Lys residues. ":1-10 and :K" selects all Lys residues in the range of residue number 1-10. ":1-10 or not :K" selects all residues 1-10, which are not Lys residues.
The wild card character "X" or "x" can be used to represent any character.
Set Operation:
Users can select multiple sets in the menu "Select > Defined Sets".
Different sets can be unioned(with "or", default), intersected(with "and"), or negated(with "not"). For example, if the "Defined Sets" menu has four sets ":1-10", ":11-20", ":5-15", and ":7-8", the command "saved atoms :1-10 or :11-20 and :5-15 not :7-8" unions all residues 1-10 and 11-20 to get the residues 1-20, then intersects with the residues 5-15 to get the residues 5-15, then exclude the residues 7-8 to get the final residues 5-6 and 9-15.
Full commands in url or command window:
Select without saving the set: select $1HHO,4N7N.A,B,C:5-10,LV,chemicals@CA,C,C*
Select and save: select $1HHO,4N7N.A,B,C:5-10,LV,chemicals@CA,C,C* | name my_name
Select:
Name:
Specification Tips:
Specification: In the selection "$1HHO,4N7N.A,B,C:5-10,LV,3AlaVal,chemicals@CA,C,C*":
"$1HHO,4N7N" uses "$" to indicate structure selection.
".A,B,C" uses "." to indicate chain selection.
":5-10,LV,3LeuVal,chemicals" uses the colon ":" to indicate residue selection. Residue selection could be residue number(5-10), one-letter IUPAC residue name abbreviations(LV), three-letter residue names(AlaVal, "3" indicates each residue name has three letters), or predefined names: "proteins", "nucleotides", "chemicals", "ions", and "water". IUPAC abbreviations can be written either as a contiguous string(e.g., ":LV"), in order to find all instances of that sequence in the structure, or they can be separated by commas(e.g., ":L,V") to select all residues of a given type in the structure(in the latter case, select all Leucine and Valine in the structure).
"@CA,C,C*" uses "@" to indicate atom name selection. "C*" selects any atom names starting with "C".
Partial definition is allowed, e.g., ":1-10" selects all residue IDs 1-10 in all chains.
Different selections can be unioned(with "or", default), intersected(with "and"), or negated(with "not"). For example, ":1-10 or :K" selects all residues 1-10 and all Lys residues. ":1-10 and :K" selects all Lys residues in the range of residue number 1-10. ":1-10 or not :K" selects all residues 1-10, which are not Lys residues.
The wild card character "X" or "x" can be used to represent any character.
Set Operation:
Users can select multiple sets in the menu "Select > Defined Sets".
Different sets can be unioned(with "or", default), intersected(with "and"), or negated(with "not"). For example, if the "Defined Sets" menu has four sets ":1-10", ":11-20", ":5-15", and ":7-8", the command "saved atoms :1-10 or :11-20 and :5-15 not :7-8" unions all residues 1-10 and 11-20 to get the residues 1-20, then intersects with the residues 5-15 to get the residues 5-15, then exclude the residues 7-8 to get the final residues 5-6 and 9-15.
Full commands in url or command window:
Select without saving the set: select $1HHO,4N7N.A,B,C:5-10,LV,chemicals@CA,C,C*
Select and save: select $1HHO,4N7N.A,B,C:5-10,LV,chemicals@CA,C,C* | name my_name
Please input PDB ID for VAST+
Note: VAST+ finds other macromolecular structures that have a similar biological unit. To do this, VAST+ takes into consideration the complete set of 3D domains that VAST identified within a query structure, throughout all of its component protein molecules, and finds other macromolecular structures that have a similar set of proteins/3D domains.
PDB ID:
Pleaes input chain or PDB file for VAST
Note: VAST identifies 3D domains (substructures) within each protein structure in the Molecular Modeling Database (MMDB), and then finds other protein structures that have one or more similar 3D domains, using purely geometric criteria. You have two ways to do a VAST search.
Option 1, search with your selection (all residues are selected by default) in the loaded structures:
Option 2, search with PDB ID and chain name: PDB ID: Chain Name:
Option 3, search with a PDB file:
Submit your selection to Foldseek
1. your selection (all residues are selected by default) in the loaded structures to Foldseek web server.
2 (Optional). Once you see the structure neighbors, you can view the alignment in iCn3D by inputing a list of PDB chain IDs or AlphaFold UniProt IDs below.
The PDB chain IDs are the same as the record names such as "1HHO_A". The UniProt ID is the text between "AF-" and "-F1". For example, the UniProt ID for the record name "AF-P69905-F1-model_v4" is "P69905".
Chain ID List:
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Please input an AlphaFold UniProt ID
Note: AlphaFold produces a per-residue confidence score (pLDDT) between 0 and 100:
Very high (pLDDT > 90) Confident (90 > pLDDT > 70) Low (70 > pLDDT > 50) Very low (pLDDT < 50)
Note: Several PDB files could be concatenated into a single PDB file. Use the line "ENDMDL" to separate PDB files.
PDB File:
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The custom JSON file on residue colors has the following format for proteins("ALA" and "ARG") and nucleotides("G" and "A"): {"ALA":"#C8C8C8", "ARG":"#145AFF", ..., "G":"#008000", "A":"#6080FF", ...}
Residue Color File:
Please input a custom color file
The custom file for the structure has two columns separated by space or tab: residue number, and score in the range of 0-100. If you click "Apply Custom Color" button, the scores 0, 50 and 100 correspond to the three colors specified below. If you click "Apply Custom Tube", the selected residues will be displayed in a style similar to "B-factor Tube".
Custom File:
1. Score to Color: 0:50: 100: or
2.
Please input a reference number file
You can define your own reference numbers in a custom file using Excel, and then export it as a CSV file. An example file is shown below with cells separated by commas.
The first row defines the reference residue numbers, which could be any strings. The 1st cell could be anything. The rest cells are reference residue numbers (e.g., 11, 21, 10C, etc.) or empty cells. Each chain has a separate row. The first cell of the second row is the chain ID "1TUP_A". The rest cells are the corresponding real residue numbers for reference residue numbers in the first row. For example, the reference numbers for residues 100, 101, and 132 in the chain 1TUP_A are 11, 12, and 22, respectively. The fourth row shows another set of reference numners for the chain "1TUP_C". It could be a chain from a different structure.
To select all residues corresponding to the reference numbers, you can simplay replace ":" with "%" in the Specification. For example, "%12" selects the residue 101 in 1TUP_A and the residue 111 in 1TUP_B. ".A%12" has the chain "A" filter and selects the residue 101 in 1TUP_A.
All chains will be aligned to the first chain in the comma-separated chain IDs. Each chain ID has the form of PDBID_chain (e.g., 1HHO_A, case sensitive) or UniprotID (e.g., P69905 for AlphaFold structures).
Chain IDs:
(Note: To align chains in custom PDB files, you could load them in "File > Open File > PDB Files (appendable)" and click "Analysis > Defined Sets". Finally select multiple chains in Defined Sets and click "File > Realign Selection".)
Align chains
All chains will be aligned to the first chain in the comma-separated chain IDs. Each chain ID has the form of PDBID_chain (e.g., 1HHO_A, case sensitive) or UniprotID (e.g., P69905 for AlphaFold structures).
Chain IDs:
The sequence alignment (followed by structure alignment) is based on residue numbers in the First/Master chain:
(Note: To align chains in custom PDB files, you could load them in "File > Open File > PDB Files (appendable)" and click "Analysis > Defined Sets". Finally select multiple chains in Defined Sets and click "File > Realign Selection".)
Align chains
All chains will be aligned to the first chain in the comma-separated chain IDs. Each chain ID has the form of PDBID_chain (e.g., 1HHO_A, case sensitive) or UniprotID (e.g., P69905 for AlphaFold structures).
Chain IDs:
Each alignment is defined as " | "-separated residue lists in one line. "10-50" means a range of residues from 10 to 50.
Realign residue by residue
Option 1:
Option 2:
All chains will be aligned to the first chain in the comma-separated chain IDs. Each chain ID has the form of PDBID_chain (e.g., 1HHO_A, case sensitive) or UniprotID (e.g., P69905 for AlphaFold structures).
Chain IDs:
Each alignment is defined as " | "-separated residue lists in one line. "10-50" means a range of residues from 10 to 50.
Mutation analysis
Please specify the mutations with a comma separated mutation list. Each mutation can be specified as "[uppercase PDB ID or AlphaFold UniProt ID]_[Chain Name]_[Residue Number]_[One Letter Mutant Residue]". E.g., the mutation of N501Y in the E chain of PDB 6M0J can be specified as "6M0J_E_501_Y". For AlphaFold structures, the "Chain ID" is "A". If you load a custom structure without PDB or UniProt ID, you can open "Seq. & Annotations" window and find the chain ID such as "stru_A". The part before the underscore is the structure ID, which can be used to specify the mutation such as "stru_A_...". Remember to choose "Show Mutation in: Current Page".
Mutations:
ID Type: PDB IDAlphaFold UniProt ID
Show Mutation in: Current PageNew Page
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SDF File:
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XYZ File:
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File type: URL in the same host:
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Note: The "biological unit" is the biochemically active form of a biomolecule,
which can range from a monomer (single protein molecule) to an oligomer of 100+ protein molecules.
The "asymmetric unit" is the raw 3D structure data resolved by X-ray crystallography, NMR, or Cryo-electron microscopy. The asymmetric unit is equivalent to the biological unit in approximately 60% of structure records. In the remaining 40% of the records, the asymmetric unit represents a portion of the biological unit that can be reconstructed using crystallographic symmetry, or it represents multiple copies of the biological unit.
Please input a list of PDB/AlphaFold IDs
List of PDB, MMDB, or AlphaFold UniProt structures:
or
Note: The "biological unit" is the biochemically active form of a biomolecule,
which can range from a monomer (single protein molecule) to an oligomer of 100+ protein molecules.
The "asymmetric unit" is the raw 3D structure data resolved by X-ray crystallography, NMR, or Cryo-electron microscopy. The asymmetric unit is equivalent to the biological unit in approximately 60% of structure records. In the remaining 40% of the records, the asymmetric unit represents a portion of the biological unit that can be reconstructed using crystallographic symmetry, or it represents multiple copies of the biological unit.
Align sequence to structure
Enter a protein sequence ID (or FASTA sequence) and the aligned protein accession, which can be found using the BLAST search with the protein sequence ID or FASTA sequence as input. If the protein accession is not a PDB chain, the corresponding AlphaFold UniProt structure is used.
Protein Sequence ID(NCBI protein accession of a sequence): or FASTA sequence:
Aligned Protein Accession (or a chain of a PDB):
Sequence to structure prediction with ESMFold
The sequence to structure prediction is done via ESM Metagenomic Atlas. The sequence should be less than 400 characters. For any sequence longer than 400, please see the discussion here.
FASTA sequence:
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Your note will be saved in the HTML file when you click "File > Save File > iCn3D PNG Image".
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Chemical SMILES:
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State file:
Use fixed version of iCn3D
Since January 6, 2021, you can show the original view with the archived version of iCn3D by pasting your URL below and click "Show Originial View". Note the version in the parameter "v" was used to replace "full.html" with "full_[v].html" in the URL.
Share Link URL:
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Selection file:
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You can load a collection of structures via a file. Here are some example files
Collection file:
Structures:
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Preference file:
Load a map file
Note: Always load a PDB file before loading map files. If you don't specify the threshold below, a default one will be chosen.
2fofc contour at default threshold or at: σ
fofc contour at default threshold or at: σ
Load a selection file via a URL
Note: Always load a PDB file before loading map files. If you don't specify the threshold below, a default one will be chosen.
2fofc contour at default threshold or at: σ URL in the same host:
fofc contour at default threshold or at: σ URL in the same host:
Note: Only the selected residues are used for DelPhi potential calculation by solving linear Poisson-Boltzmann equation.
The hydrogens and partial charges of proteins and nucleotides are added using DelPhiPKa with the Amber charge and size files. The hydrogens of ligands are added using Open Babel. The partial charges of ligands are calculated using Antechamber with the Gasteiger charge method. All partial charges are calculated at pH 7.
Lipids are treated as ligands. Please use "HETATM" instead of "ATOM " for each lipid atom in your PDB file. Each phosphate in lipids is assigned with a charge of -1. You can download PQR and modify it, or prepare your PQR file using other tools. Then load the PQR file at the menu "Analysis > Load PQR/Potential".
Grid Size: Salt Concentration: M
Surface with max potential at: kT/e(25.6mV at 298K)
Surface: Opacity: Wireframe:
Note: Only the selected residues are used for DelPhi potential calculation by solving linear Poisson-Boltzmann equation.
The hydrogens and partial charges of proteins and nucleotides are added using DelPhiPKa with the Amber charge and size files. The hydrogens of ligands are added using Open Babel. The partial charges of ligands are calculated using Antechamber with the Gasteiger charge method. All partial charges are calculated at pH 7.
Lipids are treated as ligands. Please use "HETATM" instead of "ATOM " for each lipid atom in your PDB file. Each phosphate in lipids is assigned with a charge of -1. You can download PQR and modify it, or prepare your PQR file using other tools. Then load the PQR file at the menu "Analysis > Load PQR/Potential".
Note: Always load a PDB file before loading a PQR or DelPhi potential file.
The PDB file can be loaded in the URL with "pdbid=" or at "File > Open File". The PQR file can be prepared at the menu "Analysis > Download PQR" with your modification or using other tools. The DelPhi potential file can be calculated at DelPhi Web Server and be exported as a Cube file.
Surface with max potential at: kT/e(25.6mV at 298K)
Note: Always load a PDB file before loading a PQR or DelPhi potential file.
The PDB file can be loaded in the URL with "pdbid=" or at "File > Open File". The PQR file can be prepared at the menu "Analysis > Download PQR" with your modification or using other tools. The DelPhi potential file can be calculated at DelPhi Web Server and be exported as a Cube file.
Note: Always load a PDB file before loading a PQR or DelPhi potential file.
The PDB file can be loaded in the URL with "pdbid=" or at "File > Open File". The PQR file can be prepared at the menu "Analysis > Download PQR" with your modification or using other tools. The DelPhi potential file can be calculated at DelPhi Web Server and be exported as a Cube file. The PQR or potential file can be accessed in a URL if it is located in the same host as iCn3D.
Surface with max potential at: kT/e(25.6mV at 298K)
Note: Always load a PDB file before loading a PQR or DelPhi potential file.
The PDB file can be loaded in the URL with "pdbid=" or at "File > Open File". The PQR file can be prepared at the menu "Analysis > Download PQR" with your modification or using other tools. The DelPhi potential file can be calculated at DelPhi Web Server and be exported as a Cube file. The PQR or potential file can be accessed in a URL if it is located in the same host as iCn3D.
Symmetry
Symmetry:
Dynamically symmetry calculation using SymD
Contact Map
Distance: Contact Type:
Interaction Analysis
1. Choose interaction types and their thresholds:
Hydrogen Bonds
Å
Salt Bridge/Ionic
Å
Contacts/Interactions
Å
Halogen Bonds
Å
π-Cation
Å
π-Stacking
Å
2. Select the first set:
3. Select the second set:
4.
Sort Interactions on:
to show two lines of residue nodes
to show map
with atom details
to show interactions with strength parameters in 0-200:
Helix or Sheet:
Coil or Nucleotide:
Disulfide Bonds:
Hydrogen Bonds:
Salt Bridge/Ionic:
Contacts:
Halogen Bonds:
π-Cation:
π-Stacking:
(Note: you can also adjust thresholds at #1 to add/remove interactions.)
5. and select new sets
Realign by sequence
1. Select sets below or use your current selection:
2.
Realign by structure
1. Select sets below or use your current selection.
2.
Realign two structure complexes
1. Select sets below or use your current selection:
2. Overall maximum RMSD: Å
3.
Set color spectrum across sets
1. Select sets below:
2.
Set color spectrum for residues in sets
1. Select sets below:
2.
Set color rainbow across sets
1. Select sets below:
2.
Set color rainbow for residues in sets
1. Select sets below:
2.
All interactions
Sorted interactions
2D Interaction Network
Hold Ctrl key to select multiple nodes/lines.
Green: H-Bonds; Cyan: Salt Bridge/Ionic; Grey: Contacts
Note: The following parameters will be saved in cache. You just need to set them once.
1. Shininess: (for the shininess of the 3D objects, default 40)
2. Three directional lights: Key Light: (for the light strength of the key light, default 0.8) Fill Light: (for the light strength of the fill light, default 0.4) Back Light: (for the light strength of the back light, default 0.2)
Note: The full protein sequences with gaps in MSA are listed one by one. The sequence of the structure is listed at the top. Each sequence has a title line starting with ">".
Precalculated Multiple Sequence Alignment (MSA):
Position of the first residue in Sequences & Annotations window:
Color Sequence by:
Note: Show exons for all isoforms of the protein in the same gene as specified below.
Position of the first residue in Sequences & Annotations window:
BED file:
Track Title:
Track Text (e.g., "2 G, 5-6 RR" defines a character "G" at the position 2 and two continuous characters "RR" at positions from 5 to 6. The starting position is 1):
Track Title:
Save Selection
Name:
Share Link
1. URLs Used in Browsers
Please copy one of the URLs below. They show the same result. (To add a title to share link, click "Windows > Your Note" and click "File > Share Link" again.)
Original URL with commands:
Lifelong Short URL:(To replace this URL, send a pull request to update share.html at iCn3D GitHub)
Lifelong Short URL + Window Title:(To update the window title, click "Analysis > Your Note/Window Title".)
2. Commands Used in Jupyter Noteboook
Please copy the following commands into a cell in Jupyter Notebook to show the same result. More details are at https://github.com/ncbi/icn3d/tree/master/jupyternotebook.
Select on 1D sequences: drag to select, drag again to deselect, multiple selection is allowed without Ctrl key, click "Save Selection" to save the current selection.
Select on 2D interaction diagram: click on the nodes or lines. The nodes are chains and can be united with the Ctrl key. The lines are interactions and can NOT be united. Each click on the lines selects half of the lines, i.e., select the interacting residues in one of the two chains.
Select on 3D structures: hold "Alt" and use mouse to pick, click the second time to deselect, hold "Ctrl" to union selection, hold "Shift" to select a range, press the up/down arrow to switch among atom/residue/strand/chain/structure, click "Save Selection" to save the current selection.
Save the current selection(either on 3D structure, 2D interactions, or 1D sequence): open the menu "Select -> Save Selection", specify the name and description for the selection, and click "Save".
Residue labeling: standard residue with coordinates: UPPER case letter; nonstandard residue with coordinates: the first UPPER case letter plus a period except that water residue uses the letter 'O'; residue missing coordinates: lower case letter.
Interactions
Zoom: mouse wheel; Move: left button; Select Multiple Nodes: Ctrl Key and drag an Area
Click "View > H-Bonds & Interactions" to adjust parameters and relaunch the graph
Green: H-Bonds; Cyan: Salt Bridge/Ionic; Grey: contacts; Orange: disulfide bonds
Solvent Accessible Surface Area(SASA) calculated using the EDTSurf algorithm: (0-20% out is considered "in". 50-100% out is considered "out".)
Toal: Å2
Color by surface area
Color each residue based on the percentage of solvent accessilbe surface area. The color ranges from blue, to white, to red for a percentage of 0, 35(variable), and 100, respectively.
Middle Percentage(White): %
RMSD
Buried surface area
Select residues basen on solvent accessilbe surface area
Select residue based on the percentage of solvent accessilbe surface area. The values are in the range of 0-100.
Min Percentage: % Max Percentage: %
Select residues basen on B-factor/pLDDT
Select residue based on B-factor/pLDDT. The values are in the range of 0-100.
Min B-factor/pLDDT: % Max B-factor/pLDDT: %
Legend
Distance Table
Angle Table
Translate the X,Y,Z coordinates of the structure
X: Y: Z:
Measure the angle between two vectors
Vector 1, X: Y: Z: Vector 2, X: Y: Z:
The angle is: degree.
Apply matrix to the X,Y,Z coordinates of the structure