5DMJA

Structure of the extracellular domain of the cd40 in complex with 3h56-5 dab
Total Genus 21

The genus trace: a function that shows values of genus (vertical axis) for subchains spanned between the first residue, and all other residues (shown on horizontal axis). The number of the latter residue and the genus of a given subchain are shown interactively.

Total Genus
21
sequence length
165
structure length
165
Chain Sequence
TACREKQYLINSQCCSLCQPGQKLVSDCTEFTETECLPCGESEFLDTWNRETHCHQHKYCDPNLGLRVQQKGTSETDTICTCEEGWHCTSEACESCVLHRSCSPGFGVKQIATGVSDTICEPCPVGFFSDVSSAFEKCHPWTSCETKDLVVQQAGTDKTDVVCGP

The genus matrix. At position (x,y) a genus value for a subchain spanned between x’th and y’th residue is shown. Values of the genus are represented by color, according to the scale given on the right.

Structure visualization

After clicking on a point (x,y) in the genus matrix above, a subchain from x to y is shown in color.


  Genus data interpretation
Chord Diagram
EMPTYTII1 (27-30)TIV2 (33-36)S1 (45-49)O4 (38-51)O13 (22-92)TIV3 (34-37)O1 (24-26)O3 (26-37)TII2 (42-45)O5 (41-59)TI1 (52-55)O6 (62-77)S2 (58-61)S4 (78-79)S3 (66-67)TII3 (63-66)TI2 (96-99)O7 (83-103)TI3 (113-116)S5 (89-93)S8 (119-120)O10 (125-143)S6 (102-105)TIV4 (106-109)TII4 (126-129)TIV5 (120-123)TIV6 (136-139)S7 (110-111)O8 (105-119)S9 (130-132)TIV7 (156-159)O11 (146-161)S10 (142-144)S11 (150-151)S12 (162-163)3H1 (85-87)Updating...
connected with : NaN
molecule tags Immune system/signaling protein
source organism Homo sapiens
publication title Functional Antagonism of Human CD40 Achieved by Targeting a Unique Species-Specific Epitope.
pubmed doi rcsb
molecule keywords Tumor necrosis factor receptor superfamily member 5
total genus 21
structure length 165
sequence length 165
chains with identical sequence D, F
ec nomenclature
pdb deposition date 2015-09-08

pfam database annotations

chain Pfam Accession Code Pfam Family Identifier Pfam Description
A PF00020 TNFR_c6 TNFR/NGFR cysteine-rich region
Image from the rcsb pdb (www.rcsb.org)
cath code
ClassArchitectureTopologyHomologyDomain
2.10.50.10 Mainly Beta Ribbon Tumor Necrosis Factor Receptor, subunit A; domain 2 Tumor Necrosis Factor Receptor, subunit A, domain 2 5dmjA01
2.10.50.10 Mainly Beta Ribbon Tumor Necrosis Factor Receptor, subunit A; domain 2 Tumor Necrosis Factor Receptor, subunit A, domain 2 5dmjA02
1FT4A 5CIRE 3IJ2X 4MSVB 4E4DR 3K51B 3MBWA 1EXTA 1DU3A 3QO4A 5BNQR 4I9XC 4YN0A 4FHQA 3QBQB 4OD2S 3ME2R 1TNRR 4GIQR 3WVTA 3U3QA 3U3VA 5IHLA 2UWIA 3MHDD 4KGGC 4KGQC 3THMF 3MI8D 4J6GC 1D4VA 2HEYR 3ME4A 4MXWR 4M4RA 3U3TA 1D0GR 1SG1X 2X10A 3TJEF 4RSUD 4BK4A 3ALQR 5DMJA 5L36B 3URFZ 4BK5A 4N90R 2H9GR 2AW2B 3FL7A 3QD6R 1ZA3R 3BUKC 4M4PA 3U3PA 3X3FA 1JMAB 2HEVR 3U3SA 1NCFA
chains in the Genus database with same CATH superfamily
2E4YA 1FT4A 5CIRE 3IJ2X 2E4VA 2E4UA 4MSVB 3K51B 3MBWA 4E4DR 1EXTA 1DU3A 3QO4A 5BNQR 2E4XA 2QR6A 4I9XC 4YN0A 4FHQA 3QBQB 4OD2S 3ME2R 1TNRR 4GIQR 3WVTA 3U3QA 3U3VA 5IHLA 2UWIA 3MHDD 4KGGC 4KGQC 3THMF 3MI8D 4J6GC 1D4VA 2HEYR 3ME4A 4MXWR 4M4RA 3U3TA 1D0GR 1SG1X 2X10A 3TJEF 4RSUD 4BK4A 3ALQR 5DMJA 5L36B 2E4WA 3URFZ 4N90R 4BK5A 2H9GR 2AW2B 3FL7A 3QD6R 1ZA3R 3BUKC 4M4PA 3U3PA 3X3FA 1JMAB 2HEVR 3U3SA 1NCFA
chains in the Genus database with same CATH topology
1FT4A 5CIRE 3IJ2X 4MSVB 4E4DR 3K51B 3MBWA 1EXTA 1DU3A 3QO4A 5BNQR 4I9XC 4YN0A 4FHQA 3QBQB 4OD2S 3ME2R 1TNRR 4GIQR 3WVTA 3U3QA 3U3VA 5IHLA 2UWIA 3MHDD 4KGGC 4KGQC 3THMF 3MI8D 4J6GC 1D4VA 2HEYR 3ME4A 4MXWR 4M4RA 3U3TA 1D0GR 1SG1X 2X10A 3TJEF 4RSUD 4BK4A 3ALQR 5DMJA 5L36B 3URFZ 4BK5A 4N90R 2H9GR 2AW2B 3FL7A 3QD6R 1ZA3R 3BUKC 4M4PA 3U3PA 3X3FA 1JMAB 2HEVR 3U3SA 1NCFA
chains in the Genus database with same CATH homology

  
#chains in the Genus database with same CATH superfamily
 1FT4 A;  5CIR E;  3IJ2 X;  4MSV B;  4E4D R;  3K51 B;  3MBW A;  1EXT A;  1DU3 A;  3QO4 A;  5BNQ R;  4I9X C;  4YN0 A;  4FHQ A;  3QBQ B;  4OD2 S;  3ME2 R;  1TNR R;  4GIQ R;  3WVT A;  3U3Q A;  3U3V A;  5IHL A;  2UWI A;  3MHD D;  4KGG C;  4KGQ C;  3THM F;  3MI8 D;  4J6G C;  1D4V A;  2HEY R;  3ME4 A;  4MXW R;  4M4R A;  3U3T A;  1D0G R;  1SG1 X;  2X10 A;  3TJE F;  4RSU D;  4BK4 A;  3ALQ R;  5DMJ A;  5L36 B;  3URF Z;  4BK5 A;  4N90 R;  2H9G R;  2AW2 B;  3FL7 A;  3QD6 R;  1ZA3 R;  3BUK C;  4M4P A;  3U3P A;  3X3F A;  1JMA B;  2HEV R;  3U3S A;  1NCF A; 
#chains in the Genus database with same CATH topology
 2E4Y A;  1FT4 A;  5CIR E;  3IJ2 X;  2E4V A;  2E4U A;  4MSV B;  3K51 B;  3MBW A;  4E4D R;  1EXT A;  1DU3 A;  3QO4 A;  5BNQ R;  2E4X A;  2QR6 A;  4I9X C;  4YN0 A;  4FHQ A;  3QBQ B;  4OD2 S;  3ME2 R;  1TNR R;  4GIQ R;  3WVT A;  3U3Q A;  3U3V A;  5IHL A;  2UWI A;  3MHD D;  4KGG C;  4KGQ C;  3THM F;  3MI8 D;  4J6G C;  1D4V A;  2HEY R;  3ME4 A;  4MXW R;  4M4R A;  3U3T A;  1D0G R;  1SG1 X;  2X10 A;  3TJE F;  4RSU D;  4BK4 A;  3ALQ R;  5DMJ A;  5L36 B;  2E4W A;  3URF Z;  4N90 R;  4BK5 A;  2H9G R;  2AW2 B;  3FL7 A;  3QD6 R;  1ZA3 R;  3BUK C;  4M4P A;  3U3P A;  3X3F A;  1JMA B;  2HEV R;  3U3S A;  1NCF A; 
#chains in the Genus database with same CATH homology
 1FT4 A;  5CIR E;  3IJ2 X;  4MSV B;  4E4D R;  3K51 B;  3MBW A;  1EXT A;  1DU3 A;  3QO4 A;  5BNQ R;  4I9X C;  4YN0 A;  4FHQ A;  3QBQ B;  4OD2 S;  3ME2 R;  1TNR R;  4GIQ R;  3WVT A;  3U3Q A;  3U3V A;  5IHL A;  2UWI A;  3MHD D;  4KGG C;  4KGQ C;  3THM F;  3MI8 D;  4J6G C;  1D4V A;  2HEY R;  3ME4 A;  4MXW R;  4M4R A;  3U3T A;  1D0G R;  1SG1 X;  2X10 A;  3TJE F;  4RSU D;  4BK4 A;  3ALQ R;  5DMJ A;  5L36 B;  3URF Z;  4BK5 A;  4N90 R;  2H9G R;  2AW2 B;  3FL7 A;  3QD6 R;  1ZA3 R;  3BUK C;  4M4P A;  3U3P A;  3X3F A;  1JMA B;  2HEV R;  3U3S A;  1NCF A;
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similar chains in the Genus database (?% sequence similarity)
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similar chains in the pdb database (?% sequence similarity)

  
#similar chains in the Genus database (?% sequence similarity)
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#similar chains, but unknotted
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