4E4DR

Crystal structure of mouse rankl-opg complex
Total Genus 15
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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
15
sequence length
135
structure length
135
Chain Sequence
YLHYDPETGHQLLCDKCAPGTYLKQHCTVRRKTLCVPCPDHSYTDSWHTSDECVYCSPVCKELQSVKQECNRTHNRVCECEEGRYLEIEFCLKHRSCPPGSGVVQAGTPERNTVCKKCPDGFFSGETSSKAPCIK
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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.

Chord Diagram
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molecule tags Cytokine/signaling protein
molecule keywords Tumor necrosis factor ligand superfamily member 11, soluble
publication title RANKL Employs Distinct Binding Modes to Engage RANK and the Osteoprotegerin Decoy Receptor.
pubmed doi rcsb
source organism Mus musculus
total genus 15
structure length 135
sequence length 135
ec nomenclature
pdb deposition date 2012-03-12

pfam database annotations

chain Pfam Accession Code Pfam Family Identifier Pfam Description
R 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 4e4dR01
3.10.360.30 Alpha Beta Roll Antimicrobial Peptide, Beta-defensin 2; Chain A Antimicrobial Peptide, Beta-defensin 2; Chain A 4e4dR02
5DMJA 4KGQC 1ZA3R 2H9GR 4I9XC 3URFZ 5L36B 4M4RA 3MI8D 3ME2R 3WVTA 3FL7A 3U3VA 3MBWA 4KGGC 2UWIA 3BUKC 3QBQB 4E4DR 4GIQR 4J6GC 4FHQA 3ALQR 1EXTA 1D0GR 4OD2S 3IJ2X 4BK5A 5BNQR 3MHDD 4M4PA 2X10A 3U3PA 5IHLA 3TJEF 1DU3A 2HEYR 3ME4A 4MSVB 2AW2B 5CIRE 1TNRR 3QO4A 4MXWR 4YN0A 4RSUD 3X3FA 3THMF 3U3TA 1D4VA 2HEVR 1SG1X 4N90R 1NCFA 4BK4A 3K51B 1JMAB 3U3QA 3U3SA 1FT4A 3QD6R
chains in the Genus database with same CATH superfamily
5DMJA 4KGQC 1ZA3R 2H9GR 4I9XC 3URFZ 2E4UA 5L36B 4M4RA 3MI8D 2E4VA 3ME2R 3WVTA 3FL7A 2LWLA 3U3VA 2LXOA 3MBWA 2MJKA 2E4XA 2UWIA 3BUKC 3QBQB 4KGGC 4E4DR 4GIQR 4J6GC 4FHQA 3ALQR 2E4WA 1EXTA 1D0GR 4OD2S 3IJ2X 4BK5A 5BNQR 3MHDD 4M4PA 2X10A 3U3PA 2E4YA 1KJ6A 1FD3A 5IHLA 3TJEF 1FQQA 1DU3A 2HEYR 3ME4A 4MSVB 2AW2B 5CIRE 1TNRR 3QO4A 4MXWR 2QR6A 4RSUD 4YN0A 3X3FA 3THMF 3U3TA 1FD4A 1D4VA 2HEVR 1SG1X 4N90R 1NCFA 4BK4A 3K51B 1JMAB 3U3QA 3U3SA 1FT4A 3QD6R
chains in the Genus database with same CATH topology
5DMJA 4KGQC 1ZA3R 2H9GR 4I9XC 3URFZ 5L36B 4M4RA 3MI8D 3ME2R 3WVTA 3FL7A 2LWLA 3U3VA 2LXOA 3MBWA 2MJKA 4KGGC 2UWIA 3BUKC 3QBQB 4E4DR 4GIQR 4J6GC 4FHQA 3ALQR 1EXTA 1D0GR 4OD2S 3IJ2X 4BK5A 5BNQR 3MHDD 4M4PA 2X10A 3U3PA 1KJ6A 1FD3A 5IHLA 3TJEF 1FQQA 1DU3A 2HEYR 3ME4A 4MSVB 2AW2B 5CIRE 1TNRR 3QO4A 4MXWR 4YN0A 4RSUD 3X3FA 1FD4A 3THMF 3U3TA 1D4VA 2HEVR 1SG1X 4N90R 1NCFA 4BK4A 3K51B 1JMAB 3U3QA 3U3SA 1FT4A 3QD6R
chains in the Genus database with same CATH homology


 
#chains in the Genus database with same CATH superfamily
 5DMJ A;  4KGQ C;  1ZA3 R;  2H9G R;  4I9X C;  3URF Z;  5L36 B;  4M4R A;  3MI8 D;  3ME2 R;  3WVT A;  3FL7 A;  3U3V A;  3MBW A;  4KGG C;  2UWI A;  3BUK C;  3QBQ B;  4E4D R;  4GIQ R;  4J6G C;  4FHQ A;  3ALQ R;  1EXT A;  1D0G R;  4OD2 S;  3IJ2 X;  4BK5 A;  5BNQ R;  3MHD D;  4M4P A;  2X10 A;  3U3P A;  5IHL A;  3TJE F;  1DU3 A;  2HEY R;  3ME4 A;  4MSV B;  2AW2 B;  5CIR E;  1TNR R;  3QO4 A;  4MXW R;  4YN0 A;  4RSU D;  3X3F A;  3THM F;  3U3T A;  1D4V A;  2HEV R;  1SG1 X;  4N90 R;  1NCF A;  4BK4 A;  3K51 B;  1JMA B;  3U3Q A;  3U3S A;  1FT4 A;  3QD6 R; 
#chains in the Genus database with same CATH topology
 5DMJ A;  4KGQ C;  1ZA3 R;  2H9G R;  4I9X C;  3URF Z;  2E4U A;  5L36 B;  4M4R A;  3MI8 D;  2E4V A;  3ME2 R;  3WVT A;  3FL7 A;  2LWL A;  3U3V A;  2LXO A;  3MBW A;  2MJK A;  2E4X A;  2UWI A;  3BUK C;  3QBQ B;  4KGG C;  4E4D R;  4GIQ R;  4J6G C;  4FHQ A;  3ALQ R;  2E4W A;  1EXT A;  1D0G R;  4OD2 S;  3IJ2 X;  4BK5 A;  5BNQ R;  3MHD D;  4M4P A;  2X10 A;  3U3P A;  2E4Y A;  1KJ6 A;  1FD3 A;  5IHL A;  3TJE F;  1FQQ A;  1DU3 A;  2HEY R;  3ME4 A;  4MSV B;  2AW2 B;  5CIR E;  1TNR R;  3QO4 A;  4MXW R;  2QR6 A;  4RSU D;  4YN0 A;  3X3F A;  3THM F;  3U3T A;  1FD4 A;  1D4V A;  2HEV R;  1SG1 X;  4N90 R;  1NCF A;  4BK4 A;  3K51 B;  1JMA B;  3U3Q A;  3U3S A;  1FT4 A;  3QD6 R; 
#chains in the Genus database with same CATH homology
 5DMJ A;  4KGQ C;  1ZA3 R;  2H9G R;  4I9X C;  3URF Z;  5L36 B;  4M4R A;  3MI8 D;  3ME2 R;  3WVT A;  3FL7 A;  2LWL A;  3U3V A;  2LXO A;  3MBW A;  2MJK A;  4KGG C;  2UWI A;  3BUK C;  3QBQ B;  4E4D R;  4GIQ R;  4J6G C;  4FHQ A;  3ALQ R;  1EXT A;  1D0G R;  4OD2 S;  3IJ2 X;  4BK5 A;  5BNQ R;  3MHD D;  4M4P A;  2X10 A;  3U3P A;  1KJ6 A;  1FD3 A;  5IHL A;  3TJE F;  1FQQ A;  1DU3 A;  2HEY R;  3ME4 A;  4MSV B;  2AW2 B;  5CIR E;  1TNR R;  3QO4 A;  4MXW R;  4YN0 A;  4RSU D;  3X3F A;  1FD4 A;  3THM F;  3U3T A;  1D4V A;  2HEV R;  1SG1 X;  4N90 R;  1NCF A;  4BK4 A;  3K51 B;  1JMA B;  3U3Q A;  3U3S A;  1FT4 A;  3QD6 R; 
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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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