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Conserved domains on  [gi|56554145|pdb|1U5Y|B]
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Chain B, Tumor necrosis factor ligand superfamily member 13

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

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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 ...
 7-138 1.22e-22

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: 86.63  E-value: 1.22e-22
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1U5Y_B        7 VLHLVPVNITSkadsDVTEVMWQPVLRRG---RGLEAQGDIVRVWDTGIYLLYSQVLF---HDVTFTMGQVVSREGQGRR 80
Cdd:cd00184   2 AAHLIGTNSSS----GGTGLSWESDDGRAflsGGLELQNGELVVPQDGLYYIYSQVYFrgqCCSTLSVSHVLQLRTDSYP 77

                        90       100       110       120       130       140
                ....*....|....*....|....*....|....*....|....*....|....*....|.
1U5Y_B       81 E--TLFRCIRSMPSDP-DRAYNSCYSAGVFHLHQGDIITVKIPRaNAKLSLSPHGTFLGFV 138
Cdd:cd00184  78 EpiLLLKGIRSVCSSVsEGWYNSVYLGGLFQLRAGDRLSVNVSA-PALLDLSQGTTFFGAF 137
 
Name Accession Description Interval E-value
TNF cd00184
Tumor Necrosis Factor; TNF superfamily members include the cytokines: TNF (TNF-alpha), LT ...
 7-138 1.22e-22

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: 86.63  E-value: 1.22e-22
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1U5Y_B        7 VLHLVPVNITSkadsDVTEVMWQPVLRRG---RGLEAQGDIVRVWDTGIYLLYSQVLF---HDVTFTMGQVVSREGQGRR 80
Cdd:cd00184   2 AAHLIGTNSSS----GGTGLSWESDDGRAflsGGLELQNGELVVPQDGLYYIYSQVYFrgqCCSTLSVSHVLQLRTDSYP 77

                        90       100       110       120       130       140
                ....*....|....*....|....*....|....*....|....*....|....*....|.
1U5Y_B       81 E--TLFRCIRSMPSDP-DRAYNSCYSAGVFHLHQGDIITVKIPRaNAKLSLSPHGTFLGFV 138
Cdd:cd00184  78 EpiLLLKGIRSVCSSVsEGWYNSVYLGGLFQLRAGDRLSVNVSA-PALLDLSQGTTFFGAF 137
TNF pfam00229
TNF(Tumour Necrosis Factor) family;
51-140 1.02e-08

TNF(Tumour Necrosis Factor) family;


Pssm-ID: 425540  Cd Length: 127  Bit Score: 50.00  E-value: 1.02e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1U5Y_B         51 GIYLLYSQVLFHDVTFTMGQV-----VSREG--QGRRETLFRCIRSMPS--DPDRAYNSCYSAGVFHLHQGDIITVKIPr 121
Cdd:pfam00229  29 GLYYVYSQVYFRGEGCPSGSVplthyLYKFSssYPGPVLLLKGAESPCSseNPEYWYQSIYLGGLFELRAGDRLSVNVS- 107

                          90       100
                  ....*....|....*....|
1U5Y_B        122 ANAKLSLSPHG-TFLGFVKL 140
Cdd:pfam00229 108 NPSLVDLSAPGkTYFGAFLL 127
 
Name Accession Description Interval E-value
TNF cd00184
Tumor Necrosis Factor; TNF superfamily members include the cytokines: TNF (TNF-alpha), LT ...
 7-138 1.22e-22

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: 86.63  E-value: 1.22e-22
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1U5Y_B        7 VLHLVPVNITSkadsDVTEVMWQPVLRRG---RGLEAQGDIVRVWDTGIYLLYSQVLF---HDVTFTMGQVVSREGQGRR 80
Cdd:cd00184   2 AAHLIGTNSSS----GGTGLSWESDDGRAflsGGLELQNGELVVPQDGLYYIYSQVYFrgqCCSTLSVSHVLQLRTDSYP 77

                        90       100       110       120       130       140
                ....*....|....*....|....*....|....*....|....*....|....*....|.
1U5Y_B       81 E--TLFRCIRSMPSDP-DRAYNSCYSAGVFHLHQGDIITVKIPRaNAKLSLSPHGTFLGFV 138
Cdd:cd00184  78 EpiLLLKGIRSVCSSVsEGWYNSVYLGGLFQLRAGDRLSVNVSA-PALLDLSQGTTFFGAF 137
TNF pfam00229
TNF(Tumour Necrosis Factor) family;
51-140 1.02e-08

TNF(Tumour Necrosis Factor) family;


Pssm-ID: 425540  Cd Length: 127  Bit Score: 50.00  E-value: 1.02e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1U5Y_B         51 GIYLLYSQVLFHDVTFTMGQV-----VSREG--QGRRETLFRCIRSMPS--DPDRAYNSCYSAGVFHLHQGDIITVKIPr 121
Cdd:pfam00229  29 GLYYVYSQVYFRGEGCPSGSVplthyLYKFSssYPGPVLLLKGAESPCSseNPEYWYQSIYLGGLFELRAGDRLSVNVS- 107

                          90       100
                  ....*....|....*....|
1U5Y_B        122 ANAKLSLSPHG-TFLGFVKL 140
Cdd:pfam00229 108 NPSLVDLSAPGkTYFGAFLL 127
 
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.
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