2PAUA

Crystal structure of the 5'-deoxynucleotidase yfbr mutant e72a complexed with co(2+) and damp
Total Genus 62
204060801001201401600102030405060
Genus TraceResidueGenus

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

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
3H1 (13-15)AH1 (5-11)EMPTYTI1 (19-22)TIV1 (17-20)TVIII1 (24-27)AH2 (30-52)AH3 (58-67)AH7 (127-151)AH4 (71-75)3H2 (110-112)AH5 (89-106)AH6 (113-121)TI3 (122-125)AH8 (156-170)AH9 (173-183)TI2 (67-70)TI4 (153-156)Updating...
connected with : NaN
molecule tags Hydrolase
source organism Escherichia coli
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
molecule keywords 5'-deoxynucleotidase YfbR
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
2O6IA 4ZWEA 4X9EA 4QG0A 4MDZA 4L1JA 3HI0A 2Q14A 1XX7A 4TO1A 1YNBA 4QFYA 5TK8A 3TMCA 5AO1A 5TKAA 2CQZA 5AO0A 4QG2A 4LRLA 4TO0A 4DMBA 2PARA 2FLOA 4MLNA 4TO2A 4QG1A 1VQRA 4RXPA 4TNPA 4TNQA 5AO4A 4N6WA 2HEKA 3CCGA 3I7AA 4RXRA 4MCWA 4Q7HA 4TNXA 3HC1A 3KH1A 2GZ4A 4L1JB 2DQBA 4N71A 1U6ZA 4TNRA 4TO3A 3IRHA 4L7WA 2PAQA 5AO2A 3M1TA 3NQWA 3TMBA 4L7EA 4QFZA 4RXQA 3NR1A 5TK9A 3RF0A 3P3QA 2PGSA 4RXSA 2PAUA 4MLMA 4ZWGA 3LJXA 3MEMA 4XDSA 4TNYA 4MZ7A 5AO3A 4TNZA 5TK7A 5TK6A 4TO5A 4QFXA 3TMDA 4BZBA 4BZCA 4TO4A 3BG2A 2PQ7A 1VJ7A 3MZOA 4RXOA 4R8ZA 4TO6A 4ME4A 2O08A 1YOYA 2OGIA 4QG4A 3U1NA 3TM8A
chains in the Genus database with same CATH superfamily
2O6IA 4ZWEA 4X9EA 4QG0A 4MDZA 4L1JA 3HI0A 2Q14A 1XX7A 4TO1A 1YNBA 4QFYA 5TK8A 3TMCA 5AO1A 5TKAA 2CQZA 4Q2DA 4QG2A 5AO0A 4LRLA 4TO0A 4DMBA 2PARA 2FLOA 3GW7A 3S4LA 4MLNA 4TO2A 3KQ5A 4QG1A 1VQRA 4RXPA 3SK9A 4TNPA 4TNQA 5AO4A 4N6WA 2HEKA 3CCGA 3I7AA 4RXRA 4MCWA 4Q7HA 4TNXA 4QQXA 3HC1A 3KH1A 2GZ4A 4L1JB 2DQBA 4N71A 1U6ZA 4Q2CA 4TNRA 4TO3A 3IRHA 4L7WA 2PAQA 5AO2A 3M1TA 3NQWA 3TMBA 4L7EA 4QFZA 4RXQA 3NR1A 5TK9A 3RF0A 3P3QA 2PGSA 4RXSA 2PAUA 4QQWA 4MLMA 4ZWGA 3LJXA 3MEMA 4XDSA 4TNYA 4MZ7A 5AO3A 4TNZA 5TK7A 5TK6A 4QQYA 4TO5A 4QFXA 3TMDA 4BZBA 4BZCA 4TO4A 3BG2A 2PQ7A 1VJ7A 3MZOA 4RXOA 3SKDA 4R8ZA 4QQZA 4TO6A 4ME4A 2O08A 1YOYA 2OGIA 4QG4A 3U1NA 3TM8A
chains in the Genus database with same CATH topology
2O6IA 4ZWEA 4X9EA 4QG0A 4MDZA 4L1JA 3HI0A 2Q14A 1XX7A 4TO1A 1YNBA 4QFYA 5TK8A 3TMCA 5AO1A 5TKAA 2CQZA 4Q2DA 4QG2A 5AO0A 4LRLA 4TO0A 4DMBA 2PARA 2FLOA 3GW7A 3S4LA 4MLNA 4TO2A 3KQ5A 4QG1A 1VQRA 4RXPA 3SK9A 4TNPA 4TNQA 5AO4A 4N6WA 2HEKA 3CCGA 3I7AA 4RXRA 4MCWA 4Q7HA 4TNXA 4QQXA 3HC1A 3KH1A 2GZ4A 4L1JB 2DQBA 4N71A 1U6ZA 4Q2CA 4TNRA 4TO3A 3IRHA 4L7WA 2PAQA 5AO2A 3M1TA 3NQWA 3TMBA 4L7EA 4QFZA 4RXQA 3NR1A 5TK9A 3RF0A 3P3QA 2PGSA 4RXSA 2PAUA 4QQWA 4MLMA 4ZWGA 3LJXA 3MEMA 4XDSA 4TNYA 4MZ7A 5AO3A 4TNZA 5TK7A 5TK6A 4QQYA 4TO5A 4QFXA 3TMDA 4BZBA 4BZCA 4TO4A 3BG2A 2PQ7A 1VJ7A 3MZOA 4RXOA 3SKDA 4R8ZA 4QQZA 4TO6A 4ME4A 2O08A 1YOYA 2OGIA 4QG4A 3U1NA 3TM8A
chains in the Genus database with same CATH homology


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

 
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