3VKEA

Contribution of the first k-homology domain of poly(c)-binding protein 1 to its affinity and specificity for c-rich oligonucleotides
Total Genus 23
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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
23
sequence length
76
structure length
76
Chain Sequence
b'HMLTIRLLMHGKEVGSIIGKKGESVKRIREESGARINISEGNSPERIITLTGPTNAIFKAFAMIIDKLEEDINSSW'
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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 keywords Poly(rC)-binding protein 1
molecule tags Dna binding protein/dna
source organism Homo sapiens
publication title Contribution of the first K-homology domain of poly(C)-binding protein 1 to its affinity and specificity for C-rich oligonucleotides
pubmed doi rcsb
total genus 23
structure length 76
sequence length 76
chains with identical sequence B, C, D
ec nomenclature
pdb deposition date 2011-11-15

pfam database annotations

chain Pfam Accession Code Pfam Family Identifier Pfam Description
A PF00013 KH_1 KH domain
Image from the rcsb pdb (www.rcsb.org)
cath code
ClassArchitectureTopologyHomologyDomain
3.30.1370.10 Alpha Beta 2-Layer Sandwich Ribosomal Protein S8; Chain: A, domain 1 K Homology domain, type 1 3vkeA00
2JE6I 2OPUA 2CTLA 4WALA 4JVYA 4B8TA 1J5KA 1VIHA 2AXYA 2DGRA 2MJHA 5C0XG 1WVNA 1DTJA 4LIJA 1WE8A 3AEVB 1DT4A 5JEAG 2E3UA 1J4WA 1K1GA 1ZTGA 4IFDG 2JA9A 1EC6A 1TUAA 3U1KA 2P2RA 2PY9A 2CTFA 2HH3A 4QMFB 2PQUA 1KHMA 2OPVA 2JZXA 2CTKA 1X4MA 1ZZKA 2HH2A 2JVZA 1ZZIA 4NBQA 1ZZJA 3VKEA 2FMRA 1X4NA 3L7ZC 4BA2I 2YQRA 4OO1G 1VIGA 2JEAI 4WANA 2BL5A 2ANNA 2BA0A 2ANRA 4AM3A 2CTMA 4AIMA 5K36G 2JEBI 4BA1I 2CTEA 2QNDA 2CPQA 4JVHA 3V69A 2CTJA 2Z0SA 2NN6G
chains in the Genus database with same CATH superfamily
2OPUA 3OETA 3GR5A 1VIHA 2AXYA 2MJHA 1WVNA 1DTJA 4LIJA 5LL6b 4DR3H 2UUBH 1DT4A 1ZTGA 4X65H 4B3RH 2CWHA 1HNZH 5BR8H 4DR6H 2CTFA 4QMFB 4OD6A 3J80W 3J81W 1HNXH 2PQUA 1S20A 2JZXA 1S03G 1X4MA 4DV0H 2CWFA 3L7ZC 4BA2I 2VQFH 4JV5H 4LF6H 4DR5H 2JEAI 2BL5A 4OX9H 2F4VH 4DV5H 4DV7H 3JAMW 4JI0H 4EC5A 2UXBH 4BA1I 2CTEA 1I6UA 4LF8H 4NXNH 2CPMA 4G08A 4E9JA 2M8WA 1XNQH 4X66H 4DR2H 4JVYA 4B8TA 1J5KA 5DT9A 2Y3MA 1X0AA 2LTLA 1Z2IA 2E3UA 3NCVA 4LF5H 2PT7G 2JA9A 4JI4H 4JI5H 3GKUA 3U1KA 2P2RA 2FFMA 3T1YH 4B3SH 2PY9A 4LF9H 4AQYH 1XRHA 3UOEA 1IBLH 5IT9W 4LFBH 2HH2A 3GABA 1XMOH 4YHHH 1ZZJA 4NZRM 4LF7H 4DR7H 1X4NA 1MSZA 1WTJA 1NXUA 2LRRA 2A1SA 1VIGA 1PQXA 3OTOH 1ODHA 4KHPH 2ANNA 2BA0A 2ANRA 4AIMA 1N34H 3FAUA 1X9ZA 2LTMA 4DV3H 1AN7A 1V9NA 2UXCH 1HNWH 2CPQA 4DV2H 2M6QA 4DV6H 2CTJA 3KDGA 3RF2A 1V8CA 1XMQH 1IBMH 4GKJH 4PDBA 2CTLA 2ZQEA 4B8CD 2DGRA 2VKCA 5C0XG 3AEVB 2UUAH 4JYAH 1SEIA 1J5EH 1J4WA 4IFDG 3T1HH 1EC6A 1IBKH 1VBIA 1HR0H 2HH3A 1KHMA 2G8YA 4YY3H 4JI1H 3EZJA 1ZZKA 2VQEH 2HHHH 1F0XA 3VKEA 4JI2H 2X06A 5FLXW 2ZM6H 1N33H 4NZTM 4WANA 4LF4H 1N36H 4K0KH 2CTMA 4JI3H 2D9IA 2K1HA 4DR4H 1FJGH 5A2QW 2JEBI 2QNDA 4JVHA 3J7AK 4DV4H 4LFCH 1XNRH 2JE6I 2E5LH 4WALA 5IWAH 4NXMH 1WE8A 1WHRA 3OSSD 5JEAG 1K1GA 5LMUH 2FPHX 1TUAA 4H8AA 4DR1H 2O4CA 2LF0A 2OPVA 3I0PA 4X62H 2CTKA 4JI7H 2UUCH 3QD7X 1I94H 1FKAH 2JVZA 1ZZIA 4B3TH 4NBQA 1N32H 3KDKA 4LFAH 2FMRA 2UXDH 1UG8A 3SB1A 4JI8H 2YQRA 4OO1G 4X64H 4DV1H 4DUZH 4AM3A 5K36G 4B3MH 4GKKH 4JI6H 5LMNH 4FJUA 2UU9H 3V69A 2Z0SA 4DUYH 4FJSA 2NN6G 4OCHA
chains in the Genus database with same CATH topology
2JE6I 2OPUA 2CTLA 4WALA 4JVYA 4B8TA 1J5KA 1VIHA 2AXYA 2DGRA 2MJHA 5C0XG 1WVNA 1DTJA 4LIJA 1WE8A 3AEVB 1DT4A 5JEAG 2E3UA 1J4WA 1K1GA 1ZTGA 4IFDG 2JA9A 1EC6A 1TUAA 3U1KA 2P2RA 2PY9A 2CTFA 2HH3A 4QMFB 2PQUA 1KHMA 2OPVA 2JZXA 2CTKA 1X4MA 1ZZKA 2HH2A 2JVZA 1ZZIA 4NBQA 1ZZJA 3VKEA 2FMRA 1X4NA 3L7ZC 4BA2I 2YQRA 4OO1G 1VIGA 2JEAI 4WANA 2BL5A 2ANNA 2BA0A 2ANRA 4AM3A 2CTMA 4AIMA 5K36G 2JEBI 4BA1I 2CTEA 2QNDA 2CPQA 4JVHA 3V69A 2CTJA 2Z0SA 2NN6G
chains in the Genus database with same CATH homology


 
#chains in the Genus database with same CATH superfamily
 2JE6 I;  2OPU A;  2CTL A;  4WAL A;  4JVY A;  4B8T A;  1J5K A;  1VIH A;  2AXY A;  2DGR A;  2MJH A;  5C0X G;  1WVN A;  1DTJ A;  4LIJ A;  1WE8 A;  3AEV B;  1DT4 A;  5JEA G;  2E3U A;  1J4W A;  1K1G A;  1ZTG A;  4IFD G;  2JA9 A;  1EC6 A;  1TUA A;  3U1K A;  2P2R A;  2PY9 A;  2CTF A;  2HH3 A;  4QMF B;  2PQU A;  1KHM A;  2OPV A;  2JZX A;  2CTK A;  1X4M A;  1ZZK A;  2HH2 A;  2JVZ A;  1ZZI A;  4NBQ A;  1ZZJ A;  3VKE A;  2FMR A;  1X4N A;  3L7Z C;  4BA2 I;  2YQR A;  4OO1 G;  1VIG A;  2JEA I;  4WAN A;  2BL5 A;  2ANN A;  2BA0 A;  2ANR A;  4AM3 A;  2CTM A;  4AIM A;  5K36 G;  2JEB I;  4BA1 I;  2CTE A;  2QND A;  2CPQ A;  4JVH A;  3V69 A;  2CTJ A;  2Z0S A;  2NN6 G; 
#chains in the Genus database with same CATH topology
 2OPU A;  3OET A;  3GR5 A;  1VIH A;  2AXY A;  2MJH A;  1WVN A;  1DTJ A;  4LIJ A;  5LL6 b;  4DR3 H;  2UUB H;  1DT4 A;  1ZTG A;  4X65 H;  4B3R H;  2CWH A;  1HNZ H;  5BR8 H;  4DR6 H;  2CTF A;  4QMF B;  4OD6 A;  3J80 W;  3J81 W;  1HNX H;  2PQU A;  1S20 A;  2JZX A;  1S03 G;  1X4M A;  4DV0 H;  2CWF A;  3L7Z C;  4BA2 I;  2VQF H;  4JV5 H;  4LF6 H;  4DR5 H;  2JEA I;  2BL5 A;  4OX9 H;  2F4V H;  4DV5 H;  4DV7 H;  3JAM W;  4JI0 H;  4EC5 A;  2UXB H;  4BA1 I;  2CTE A;  1I6U A;  4LF8 H;  4NXN H;  2CPM A;  4G08 A;  4E9J A;  2M8W A;  1XNQ H;  4X66 H;  4DR2 H;  4JVY A;  4B8T A;  1J5K A;  5DT9 A;  2Y3M A;  1X0A A;  2LTL A;  1Z2I A;  2E3U A;  3NCV A;  4LF5 H;  2PT7 G;  2JA9 A;  4JI4 H;  4JI5 H;  3GKU A;  3U1K A;  2P2R A;  2FFM A;  3T1Y H;  4B3S H;  2PY9 A;  4LF9 H;  4AQY H;  1XRH A;  3UOE A;  1IBL H;  5IT9 W;  4LFB H;  2HH2 A;  3GAB A;  1XMO H;  4YHH H;  1ZZJ A;  4NZR M;  4LF7 H;  4DR7 H;  1X4N A;  1MSZ A;  1WTJ A;  1NXU A;  2LRR A;  2A1S A;  1VIG A;  1PQX A;  3OTO H;  1ODH A;  4KHP H;  2ANN A;  2BA0 A;  2ANR A;  4AIM A;  1N34 H;  3FAU A;  1X9Z A;  2LTM A;  4DV3 H;  1AN7 A;  1V9N A;  2UXC H;  1HNW H;  2CPQ A;  4DV2 H;  2M6Q A;  4DV6 H;  2CTJ A;  3KDG A;  3RF2 A;  1V8C A;  1XMQ H;  1IBM H;  4GKJ H;  4PDB A;  2CTL A;  2ZQE A;  4B8C D;  2DGR A;  2VKC A;  5C0X G;  3AEV B;  2UUA H;  4JYA H;  1SEI A;  1J5E H;  1J4W A;  4IFD G;  3T1H H;  1EC6 A;  1IBK H;  1VBI A;  1HR0 H;  2HH3 A;  1KHM A;  2G8Y A;  4YY3 H;  4JI1 H;  3EZJ A;  1ZZK A;  2VQE H;  2HHH H;  1F0X A;  3VKE A;  4JI2 H;  2X06 A;  5FLX W;  2ZM6 H;  1N33 H;  4NZT M;  4WAN A;  4LF4 H;  1N36 H;  4K0K H;  2CTM A;  4JI3 H;  2D9I A;  2K1H A;  4DR4 H;  1FJG H;  5A2Q W;  2JEB I;  2QND A;  4JVH A;  3J7A K;  4DV4 H;  4LFC H;  1XNR H;  2JE6 I;  2E5L H;  4WAL A;  5IWA H;  4NXM H;  1WE8 A;  1WHR A;  3OSS D;  5JEA G;  1K1G A;  5LMU H;  2FPH X;  1TUA A;  4H8A A;  4DR1 H;  2O4C A;  2LF0 A;  2OPV A;  3I0P A;  4X62 H;  2CTK A;  4JI7 H;  2UUC H;  3QD7 X;  1I94 H;  1FKA H;  2JVZ A;  1ZZI A;  4B3T H;  4NBQ A;  1N32 H;  3KDK A;  4LFA H;  2FMR A;  2UXD H;  1UG8 A;  3SB1 A;  4JI8 H;  2YQR A;  4OO1 G;  4X64 H;  4DV1 H;  4DUZ H;  4AM3 A;  5K36 G;  4B3M H;  4GKK H;  4JI6 H;  5LMN H;  4FJU A;  2UU9 H;  3V69 A;  2Z0S A;  4DUY H;  4FJS A;  2NN6 G;  4OCH A; 
#chains in the Genus database with same CATH homology
 2JE6 I;  2OPU A;  2CTL A;  4WAL A;  4JVY A;  4B8T A;  1J5K A;  1VIH A;  2AXY A;  2DGR A;  2MJH A;  5C0X G;  1WVN A;  1DTJ A;  4LIJ A;  1WE8 A;  3AEV B;  1DT4 A;  5JEA G;  2E3U A;  1J4W A;  1K1G A;  1ZTG A;  4IFD G;  2JA9 A;  1EC6 A;  1TUA A;  3U1K A;  2P2R A;  2PY9 A;  2CTF A;  2HH3 A;  4QMF B;  2PQU A;  1KHM A;  2OPV A;  2JZX A;  2CTK A;  1X4M A;  1ZZK A;  2HH2 A;  2JVZ A;  1ZZI A;  4NBQ A;  1ZZJ A;  3VKE A;  2FMR A;  1X4N A;  3L7Z C;  4BA2 I;  2YQR A;  4OO1 G;  1VIG A;  2JEA I;  4WAN A;  2BL5 A;  2ANN A;  2BA0 A;  2ANR A;  4AM3 A;  2CTM A;  4AIM A;  5K36 G;  2JEB I;  4BA1 I;  2CTE A;  2QND A;  2CPQ A;  4JVH A;  3V69 A;  2CTJ A;  2Z0S A;  2NN6 G; 
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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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