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


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