NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|27065175|pdb|1KD7|C]
View 

Chain C, Tumor Necrosis Factor Ligand Superfamily Member 13b

Protein Classification

TNF domain-containing protein( domain architecture ID 10075925)

TNF domain-containing protein similar to Homo sapiens lymphotoxin-alpha, which acts as cytokine that in its homotrimeric form binds to TNFRSF1A/TNFR1, TNFRSF1B/TNFBR and TNFRSF14/HVEM

Graphical summary

 Zoom to residue level

show extra options »

Show site features     Horizontal zoom: ×

List of domain hits

 Name Accession Description Interval E-value
TNF cd00184
Tumor Necrosis Factor; TNF superfamily members include the cytokines: TNF (TNF-alpha), LT ...
 25-161 6.07e-25

Tumor Necrosis Factor; TNF superfamily members include the cytokines: TNF (TNF-alpha), LT (lymphotoxin-alpha, TNF-beta), CD40 ligand, Apo2L (TRAIL), Fas ligand, and osteoprotegerin (OPG) ligand. These proteins generally have an intracellular N-terminal domain, a short transmembrane segment, an extracellular stalk, and a globular TNF-like extracellular domain of about 150 residues. They initiate apoptosis by binding to related receptors, some of which have intracellular death domains. They generally form homo- or hetero- trimeric complexes.TNF cytokines bind one elongated receptor molecule along each of three clefts formed by neighboring monomers of the trimer with ligand trimerization a requiste for receptor binding.


:

Pssm-ID: 238108  Cd Length: 137  Bit Score: 93.18  E-value: 6.07e-25
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1KD7_C       25 CLQLIADSETPTiqkgsYTFVPWL----LSFKRGsALEEKENKILVKETGYFFIYGQVLYTDK---TYAMGHLIQRKKVH 97
Cdd:cd00184   2 AAHLIGTNSSSG-----GTGLSWEsddgRAFLSG-GLELQNGELVVPQDGLYYIYSQVYFRGQccsTLSVSHVLQLRTDS 75

                        90       100       110       120       130       140
                ....*....|....*....|....*....|....*....|....*....|....*....|....*..
1KD7_C       98 VfgdeLSLVTLFRCIQNMPETLP---NNSCYSAGIAKLEEGDELQLAIPReNAQISLDGDVTFFGAL 161
Cdd:cd00184  76 Y----PEPILLLKGIRSVCSSVSegwYNSVYLGGLFQLRAGDRLSVNVSA-PALLDLSQGTTFFGAF 137
 
Name Accession Description Interval E-value
TNF cd00184
Tumor Necrosis Factor; TNF superfamily members include the cytokines: TNF (TNF-alpha), LT ...
 25-161 6.07e-25

Tumor Necrosis Factor; TNF superfamily members include the cytokines: TNF (TNF-alpha), LT (lymphotoxin-alpha, TNF-beta), CD40 ligand, Apo2L (TRAIL), Fas ligand, and osteoprotegerin (OPG) ligand. These proteins generally have an intracellular N-terminal domain, a short transmembrane segment, an extracellular stalk, and a globular TNF-like extracellular domain of about 150 residues. They initiate apoptosis by binding to related receptors, some of which have intracellular death domains. They generally form homo- or hetero- trimeric complexes.TNF cytokines bind one elongated receptor molecule along each of three clefts formed by neighboring monomers of the trimer with ligand trimerization a requiste for receptor binding.


Pssm-ID: 238108  Cd Length: 137  Bit Score: 93.18  E-value: 6.07e-25
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1KD7_C       25 CLQLIADSETPTiqkgsYTFVPWL----LSFKRGsALEEKENKILVKETGYFFIYGQVLYTDK---TYAMGHLIQRKKVH 97
Cdd:cd00184   2 AAHLIGTNSSSG-----GTGLSWEsddgRAFLSG-GLELQNGELVVPQDGLYYIYSQVYFRGQccsTLSVSHVLQLRTDS 75

                        90       100       110       120       130       140
                ....*....|....*....|....*....|....*....|....*....|....*....|....*..
1KD7_C       98 VfgdeLSLVTLFRCIQNMPETLP---NNSCYSAGIAKLEEGDELQLAIPReNAQISLDGDVTFFGAL 161
Cdd:cd00184  76 Y----PEPILLLKGIRSVCSSVSegwYNSVYLGGLFQLRAGDRLSVNVSA-PALLDLSQGTTFFGAF 137
TNF pfam00229
TNF(Tumour Necrosis Factor) family;
60-163 4.08e-08

TNF(Tumour Necrosis Factor) family;


Pssm-ID: 425540  Cd Length: 127  Bit Score: 49.23  E-value: 4.08e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1KD7_C         60 KENKILVKETGYFFIYGQVLYTDKTYAMG-----HLIQRKKVHVFGDelslVTLFRCIQNMPETLPN----NSCYSAGIA 130
Cdd:pfam00229  19 SNGELVVPQAGLYYVYSQVYFRGEGCPSGsvpltHYLYKFSSSYPGP----VLLLKGAESPCSSENPeywyQSIYLGGLF 94

                          90       100       110
                  ....*....|....*....|....*....|...
1KD7_C        131 KLEEGDELQLAIPRENAQISLDGDVTFFGALKL 163
Cdd:pfam00229  95 ELRAGDRLSVNVSNPSLVDLSAPGKTYFGAFLL 127
TNF smart00207
Tumour necrosis factor family; Family of cytokines that form homotrimeric or heterotrimeric ...
 55-163 2.14e-06

Tumour necrosis factor family; Family of cytokines that form homotrimeric or heterotrimeric complexes. TNF mediates mature T-cell receptor-induced apoptosis through the p75 TNF receptor.


Pssm-ID: 214557  Cd Length: 125  Bit Score: 44.65  E-value: 2.14e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1KD7_C          55 SALEEKENKILVKETGYFFIYGQVLYTDKTYAMGHLIQRKKVHVFG----DELSLVTLFRCIqNMPETLP-NNSCYSAGI 129
Cdd:smart00207  14 SGMELQNGELVVPRDGLYYIYSQVYFRGQGCNGKSVELSLSLHLRKpsypLPLLLLEAARSS-CWSASSAwKDSVYLGGL 92

                           90       100       110
                   ....*....|....*....|....*....|....
1KD7_C         130 AKLEEGDELQLAIpRENAQISLDGDVTFFGALKL 163
Cdd:smart00207  93 FPLTAGDRLSVNV-TEPSLVDLAPGATFFGAFLV 125
 
Name Accession Description Interval E-value
TNF cd00184
Tumor Necrosis Factor; TNF superfamily members include the cytokines: TNF (TNF-alpha), LT ...
 25-161 6.07e-25

Tumor Necrosis Factor; TNF superfamily members include the cytokines: TNF (TNF-alpha), LT (lymphotoxin-alpha, TNF-beta), CD40 ligand, Apo2L (TRAIL), Fas ligand, and osteoprotegerin (OPG) ligand. These proteins generally have an intracellular N-terminal domain, a short transmembrane segment, an extracellular stalk, and a globular TNF-like extracellular domain of about 150 residues. They initiate apoptosis by binding to related receptors, some of which have intracellular death domains. They generally form homo- or hetero- trimeric complexes.TNF cytokines bind one elongated receptor molecule along each of three clefts formed by neighboring monomers of the trimer with ligand trimerization a requiste for receptor binding.


Pssm-ID: 238108  Cd Length: 137  Bit Score: 93.18  E-value: 6.07e-25
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1KD7_C       25 CLQLIADSETPTiqkgsYTFVPWL----LSFKRGsALEEKENKILVKETGYFFIYGQVLYTDK---TYAMGHLIQRKKVH 97
Cdd:cd00184   2 AAHLIGTNSSSG-----GTGLSWEsddgRAFLSG-GLELQNGELVVPQDGLYYIYSQVYFRGQccsTLSVSHVLQLRTDS 75

                        90       100       110       120       130       140
                ....*....|....*....|....*....|....*....|....*....|....*....|....*..
1KD7_C       98 VfgdeLSLVTLFRCIQNMPETLP---NNSCYSAGIAKLEEGDELQLAIPReNAQISLDGDVTFFGAL 161
Cdd:cd00184  76 Y----PEPILLLKGIRSVCSSVSegwYNSVYLGGLFQLRAGDRLSVNVSA-PALLDLSQGTTFFGAF 137
TNF pfam00229
TNF(Tumour Necrosis Factor) family;
60-163 4.08e-08

TNF(Tumour Necrosis Factor) family;


Pssm-ID: 425540  Cd Length: 127  Bit Score: 49.23  E-value: 4.08e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1KD7_C         60 KENKILVKETGYFFIYGQVLYTDKTYAMG-----HLIQRKKVHVFGDelslVTLFRCIQNMPETLPN----NSCYSAGIA 130
Cdd:pfam00229  19 SNGELVVPQAGLYYVYSQVYFRGEGCPSGsvpltHYLYKFSSSYPGP----VLLLKGAESPCSSENPeywyQSIYLGGLF 94

                          90       100       110
                  ....*....|....*....|....*....|...
1KD7_C        131 KLEEGDELQLAIPRENAQISLDGDVTFFGALKL 163
Cdd:pfam00229  95 ELRAGDRLSVNVSNPSLVDLSAPGKTYFGAFLL 127
TNF smart00207
Tumour necrosis factor family; Family of cytokines that form homotrimeric or heterotrimeric ...
 55-163 2.14e-06

Tumour necrosis factor family; Family of cytokines that form homotrimeric or heterotrimeric complexes. TNF mediates mature T-cell receptor-induced apoptosis through the p75 TNF receptor.


Pssm-ID: 214557  Cd Length: 125  Bit Score: 44.65  E-value: 2.14e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1KD7_C          55 SALEEKENKILVKETGYFFIYGQVLYTDKTYAMGHLIQRKKVHVFG----DELSLVTLFRCIqNMPETLP-NNSCYSAGI 129
Cdd:smart00207  14 SGMELQNGELVVPRDGLYYIYSQVYFRGQGCNGKSVELSLSLHLRKpsypLPLLLLEAARSS-CWSASSAwKDSVYLGGL 92

                           90       100       110
                   ....*....|....*....|....*....|....
1KD7_C         130 AKLEEGDELQLAIpRENAQISLDGDVTFFGALKL 163
Cdd:smart00207  93 FPLTAGDRLSVNV-TEPSLVDLAPGATFFGAFLV 125
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
  • Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
Help | Disclaimer | Write to the Help Desk
NCBI | NLM | NIH