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


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