2PAUA

Crystal structure of the 5'-deoxynucleotidase yfbr mutant e72a complexed with co(2+) and damp
Total Genus 62
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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
62
sequence length
183
structure length
176
Chain Sequence
SHFFAHLSRLKLINRWPLMRNVRTENVSEHSLQVAMVAHALAAIKNRKFGGNVNAERIALLAMYHDASAVLTGDLPTPIAQEYKAIEKIAQQKLVDMVPEELRDIFAPLIDEHAYSDEEKSLVKQADALCAYLKCLEELAAGNNEFLLAKTRLEATLEARRSQEMDYFMEIFVPSF
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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 Hydrolase
molecule keywords 5'-deoxynucleotidase YfbR
publication title Structural insight into the mechanism of substrate specificity and catalytic activity of an HD-domain phosphohydrolase: the 5'-deoxyribonucleotidase YfbR from Escherichia coli.
pubmed doi rcsb
source organism Escherichia coli
total genus 62
structure length 176
sequence length 183
chains with identical sequence B
ec nomenclature ec 3.1.3.89: 5'-deoxynucleotidase.
pdb deposition date 2007-03-27

pfam database annotations

chain Pfam Accession Code Pfam Family Identifier Pfam Description
A PF01966 HD HD domain
Image from the rcsb pdb (www.rcsb.org)
cath code
ClassArchitectureTopologyHomologyDomain
1.10.3210.10 Mainly Alpha Orthogonal Bundle Hypothetical protein af1432 Hypothetical protein af1432 2pauA00
4N71A 4TO3A 4QG0A 3TMCA 1XX7A 4ZWGA 4TNQA 4DMBA 5AO2A 3M1TA 3I7AA 2Q14A 4RXQA 3NQWA 5AO4A 4Q7HA 4MCWA 5TK8A 4L1JB 4L1JA 5AO3A 4RXRA 4TNYA 4BZCA 2PGSA 3TMBA 3TM8A 3NR1A 4LRLA 4TO0A 4XDSA 4TNPA 2PQ7A 5AO1A 1YNBA 5TK9A 4TO2A 2DQBA 4TNXA 4L7WA 3MZOA 3HC1A 4ZWEA 2PAUA 3TMDA 2O6IA 4N6WA 4X9EA 2GZ4A 4MDZA 4RXPA 5TK6A 4MZ7A 3MEMA 4R8ZA 3CCGA 1VQRA 1YOYA 4QG4A 4TO6A 4QG1A 1U6ZA 4TNRA 3P3QA 4MLNA 3RF0A 4BZBA 4TO1A 4QG2A 5TK7A 5TKAA 4QFZA 3HI0A 2FLOA 4QFYA 4RXOA 4TO5A 2OGIA 3BG2A 1VJ7A 2O08A 4MLMA 4QFXA 4TO4A 4RXSA 2HEKA 2PAQA 2CQZA 4TNZA 3IRHA 4ME4A 4L7EA 3KH1A 2PARA 5AO0A 3LJXA 3U1NA
chains in the Genus database with same CATH superfamily
4QQWA 4N71A 4TO3A 4Q2DA 4QG0A 3TMCA 1XX7A 3SKDA 4ZWGA 4TNQA 4DMBA 5AO2A 3M1TA 3I7AA 2Q14A 4RXQA 3NQWA 5AO4A 4Q7HA 4MCWA 5TK8A 4L1JB 4L1JA 5AO3A 4RXRA 4TNYA 4BZCA 2PGSA 3KQ5A 3TMBA 3TM8A 3NR1A 4LRLA 4TO0A 4QQYA 4XDSA 4TNPA 2PQ7A 5AO1A 3GW7A 1YNBA 5TK9A 4TO2A 2DQBA 4TNXA 4L7WA 4QQZA 3MZOA 3HC1A 4ZWEA 2PAUA 3TMDA 2O6IA 4N6WA 3SK9A 4X9EA 2GZ4A 4MDZA 4RXPA 5TK6A 4MZ7A 3MEMA 4R8ZA 3CCGA 1VQRA 3S4LA 1YOYA 4QG4A 4TO6A 4QG1A 1U6ZA 4TNRA 3P3QA 4MLNA 3RF0A 4BZBA 4TO1A 4QG2A 4Q2CA 5TK7A 5TKAA 4QFZA 3HI0A 2FLOA 4QFYA 4RXOA 4TO5A 2OGIA 3BG2A 1VJ7A 2O08A 4MLMA 4QFXA 4TO4A 4RXSA 2HEKA 2PAQA 2CQZA 4TNZA 3IRHA 4ME4A 4L7EA 3KH1A 4QQXA 2PARA 5AO0A 3LJXA 3U1NA
chains in the Genus database with same CATH topology
4QQWA 4N71A 4TO3A 4Q2DA 4QG0A 3TMCA 1XX7A 3SKDA 4ZWGA 4TNQA 4DMBA 5AO2A 3M1TA 3I7AA 2Q14A 4RXQA 3NQWA 5AO4A 4Q7HA 4MCWA 5TK8A 4L1JB 4L1JA 5AO3A 4RXRA 4TNYA 4BZCA 2PGSA 3KQ5A 3TMBA 3TM8A 3NR1A 4LRLA 4TO0A 4QQYA 4XDSA 4TNPA 2PQ7A 5AO1A 3GW7A 1YNBA 5TK9A 4TO2A 2DQBA 4TNXA 4L7WA 4QQZA 3MZOA 3HC1A 4ZWEA 2PAUA 3TMDA 2O6IA 4N6WA 3SK9A 4X9EA 2GZ4A 4MDZA 4RXPA 5TK6A 4MZ7A 3MEMA 4R8ZA 3CCGA 1VQRA 3S4LA 1YOYA 4QG4A 4TO6A 4QG1A 1U6ZA 4TNRA 3P3QA 4MLNA 3RF0A 4BZBA 4TO1A 4QG2A 4Q2CA 5TK7A 5TKAA 4QFZA 3HI0A 2FLOA 4QFYA 4RXOA 4TO5A 2OGIA 3BG2A 1VJ7A 2O08A 4MLMA 4QFXA 4TO4A 4RXSA 2HEKA 2PAQA 2CQZA 4TNZA 3IRHA 4ME4A 4L7EA 3KH1A 4QQXA 2PARA 5AO0A 3LJXA 3U1NA
chains in the Genus database with same CATH homology


 
#chains in the Genus database with same CATH superfamily
 4N71 A;  4TO3 A;  4QG0 A;  3TMC A;  1XX7 A;  4ZWG A;  4TNQ A;  4DMB A;  5AO2 A;  3M1T A;  3I7A A;  2Q14 A;  4RXQ A;  3NQW A;  5AO4 A;  4Q7H A;  4MCW A;  5TK8 A;  4L1J B;  4L1J A;  5AO3 A;  4RXR A;  4TNY A;  4BZC A;  2PGS A;  3TMB A;  3TM8 A;  3NR1 A;  4LRL A;  4TO0 A;  4XDS A;  4TNP A;  2PQ7 A;  5AO1 A;  1YNB A;  5TK9 A;  4TO2 A;  2DQB A;  4TNX A;  4L7W A;  3MZO A;  3HC1 A;  4ZWE A;  2PAU A;  3TMD A;  2O6I A;  4N6W A;  4X9E A;  2GZ4 A;  4MDZ A;  4RXP A;  5TK6 A;  4MZ7 A;  3MEM A;  4R8Z A;  3CCG A;  1VQR A;  1YOY A;  4QG4 A;  4TO6 A;  4QG1 A;  1U6Z A;  4TNR A;  3P3Q A;  4MLN A;  3RF0 A;  4BZB A;  4TO1 A;  4QG2 A;  5TK7 A;  5TKA A;  4QFZ A;  3HI0 A;  2FLO A;  4QFY A;  4RXO A;  4TO5 A;  2OGI A;  3BG2 A;  1VJ7 A;  2O08 A;  4MLM A;  4QFX A;  4TO4 A;  4RXS A;  2HEK A;  2PAQ A;  2CQZ A;  4TNZ A;  3IRH A;  4ME4 A;  4L7E A;  3KH1 A;  2PAR A;  5AO0 A;  3LJX A;  3U1N A; 
#chains in the Genus database with same CATH topology
 4QQW A;  4N71 A;  4TO3 A;  4Q2D A;  4QG0 A;  3TMC A;  1XX7 A;  3SKD A;  4ZWG A;  4TNQ A;  4DMB A;  5AO2 A;  3M1T A;  3I7A A;  2Q14 A;  4RXQ A;  3NQW A;  5AO4 A;  4Q7H A;  4MCW A;  5TK8 A;  4L1J B;  4L1J A;  5AO3 A;  4RXR A;  4TNY A;  4BZC A;  2PGS A;  3KQ5 A;  3TMB A;  3TM8 A;  3NR1 A;  4LRL A;  4TO0 A;  4QQY A;  4XDS A;  4TNP A;  2PQ7 A;  5AO1 A;  3GW7 A;  1YNB A;  5TK9 A;  4TO2 A;  2DQB A;  4TNX A;  4L7W A;  4QQZ A;  3MZO A;  3HC1 A;  4ZWE A;  2PAU A;  3TMD A;  2O6I A;  4N6W A;  3SK9 A;  4X9E A;  2GZ4 A;  4MDZ A;  4RXP A;  5TK6 A;  4MZ7 A;  3MEM A;  4R8Z A;  3CCG A;  1VQR A;  3S4L A;  1YOY A;  4QG4 A;  4TO6 A;  4QG1 A;  1U6Z A;  4TNR A;  3P3Q A;  4MLN A;  3RF0 A;  4BZB A;  4TO1 A;  4QG2 A;  4Q2C A;  5TK7 A;  5TKA A;  4QFZ A;  3HI0 A;  2FLO A;  4QFY A;  4RXO A;  4TO5 A;  2OGI A;  3BG2 A;  1VJ7 A;  2O08 A;  4MLM A;  4QFX A;  4TO4 A;  4RXS A;  2HEK A;  2PAQ A;  2CQZ A;  4TNZ A;  3IRH A;  4ME4 A;  4L7E A;  3KH1 A;  4QQX A;  2PAR A;  5AO0 A;  3LJX A;  3U1N A; 
#chains in the Genus database with same CATH homology
 4QQW A;  4N71 A;  4TO3 A;  4Q2D A;  4QG0 A;  3TMC A;  1XX7 A;  3SKD A;  4ZWG A;  4TNQ A;  4DMB A;  5AO2 A;  3M1T A;  3I7A A;  2Q14 A;  4RXQ A;  3NQW A;  5AO4 A;  4Q7H A;  4MCW A;  5TK8 A;  4L1J B;  4L1J A;  5AO3 A;  4RXR A;  4TNY A;  4BZC A;  2PGS A;  3KQ5 A;  3TMB A;  3TM8 A;  3NR1 A;  4LRL A;  4TO0 A;  4QQY A;  4XDS A;  4TNP A;  2PQ7 A;  5AO1 A;  3GW7 A;  1YNB A;  5TK9 A;  4TO2 A;  2DQB A;  4TNX A;  4L7W A;  4QQZ A;  3MZO A;  3HC1 A;  4ZWE A;  2PAU A;  3TMD A;  2O6I A;  4N6W A;  3SK9 A;  4X9E A;  2GZ4 A;  4MDZ A;  4RXP A;  5TK6 A;  4MZ7 A;  3MEM A;  4R8Z A;  3CCG A;  1VQR A;  3S4L A;  1YOY A;  4QG4 A;  4TO6 A;  4QG1 A;  1U6Z A;  4TNR A;  3P3Q A;  4MLN A;  3RF0 A;  4BZB A;  4TO1 A;  4QG2 A;  4Q2C A;  5TK7 A;  5TKA A;  4QFZ A;  3HI0 A;  2FLO A;  4QFY A;  4RXO A;  4TO5 A;  2OGI A;  3BG2 A;  1VJ7 A;  2O08 A;  4MLM A;  4QFX A;  4TO4 A;  4RXS A;  2HEK A;  2PAQ A;  2CQZ A;  4TNZ A;  3IRH A;  4ME4 A;  4L7E A;  3KH1 A;  4QQX A;  2PAR A;  5AO0 A;  3LJX A;  3U1N 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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