2PAQA

Crystal structure of the 5'-deoxynucleotidase yfbr
Total Genus 54

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
54
sequence length
186
structure length
177
Chain Sequence
KQSHFFAHLSRLKLINRWPLMRNVRTENVSEHSLQVAMVAHALAAIKNRKFGGNVNAERIALLAMYHDASEVLTGDLPTPQEYKAIEKIAQQKLVDMVPEELRDIFAPLIDEHAYSDEEKSLVKQADALCAYLKCLEELAAGNNEFLLAKTRLEATLEARRSQEMDYFMEIFVPSFH

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)EMPTYS2 (28-29)S1 (17-18)TVIII1 (24-27)AH7 (127-151)AH2 (30-52)TIV2 (122-125)AH3 (58-65)TI1 (67-70)AH4 (71-75)AH6 (113-120)AH8 (156-170)TI2 (153-156)AH1 (5-11)3H2 (110-112)AH5 (92-106)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 54
structure length 177
sequence length 186
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 2paqA00
4MDZA 4TNRA 4LRLA 4RXSA 4TO2A 1YOYA 3BG2A 2O08A 3LJXA 4TO4A 2OGIA 2PQ7A 3NR1A 4QG4A 4QG0A 3U1NA 4ZWGA 4TO3A 2O6IA 1YNBA 5AO2A 4X9EA 3TMDA 4XDSA 5TK6A 4L1JB 4TO1A 2HEKA 4QG1A 5AO4A 4TNZA 3HC1A 2CQZA 5AO0A 1VQRA 3MEMA 4BZCA 1VJ7A 4BZBA 4QFYA 4Q7HA 3HI0A 4TNQA 2Q14A 5AO3A 2PAQA 3P3QA 4MLMA 4ME4A 4TNPA 3CCGA 3IRHA 3RF0A 4RXRA 4MZ7A 4L7WA 3TM8A 1XX7A 5AO1A 4QFZA 2DQBA 2FLOA 1U6ZA 5TKAA 3I7AA 4L1JA 4TNYA 4DMBA 2PARA 4N6WA 3NQWA 4TO0A 3KH1A 4TO6A 4RXOA 4MCWA 5TK9A 4L7EA 4MLNA 5TK8A 2GZ4A 4TO5A 3TMCA 4R8ZA 3MZOA 4TNXA 4QG2A 2PGSA 4RXQA 4RXPA 4ZWEA 3M1TA 4QFXA 3TMBA 5TK7A 4N71A 2PAUA
chains in the Genus database with same CATH superfamily
4MDZA 4TNRA 4Q2CA 4LRLA 4RXSA 4TO2A 1YOYA 3BG2A 2O08A 3SKDA 3LJXA 4TO4A 2OGIA 2PQ7A 4QQXA 3NR1A 4QG4A 4QG0A 3U1NA 4ZWGA 4TO3A 2O6IA 1YNBA 5AO2A 4X9EA 3TMDA 4QQYA 4XDSA 5TK6A 4L1JB 4TO1A 2HEKA 4QG1A 5AO4A 4TNZA 3HC1A 2CQZA 5AO0A 1VQRA 3MEMA 4BZCA 1VJ7A 4Q2DA 4BZBA 4QFYA 4Q7HA 3HI0A 4TNQA 2Q14A 5AO3A 2PAQA 3P3QA 4MLMA 4ME4A 4TNPA 3CCGA 3IRHA 3RF0A 4RXRA 4MZ7A 4L7WA 3TM8A 1XX7A 5AO1A 4QFZA 2DQBA 2FLOA 3SK9A 1U6ZA 5TKAA 3I7AA 4L1JA 3GW7A 4TNYA 4DMBA 3KQ5A 2PARA 4N6WA 3NQWA 4TO0A 3KH1A 4TO6A 4RXOA 4MCWA 5TK9A 4L7EA 4MLNA 4QQWA 5TK8A 2GZ4A 4TO5A 4QQZA 3TMCA 4R8ZA 3MZOA 4TNXA 4QG2A 2PGSA 4RXQA 4RXPA 4ZWEA 3M1TA 4QFXA 3S4LA 3TMBA 5TK7A 4N71A 2PAUA
chains in the Genus database with same CATH topology
4MDZA 4TNRA 4Q2CA 4LRLA 4RXSA 4TO2A 1YOYA 3BG2A 2O08A 3SKDA 3LJXA 4TO4A 2OGIA 2PQ7A 4QQXA 3NR1A 4QG4A 4QG0A 3U1NA 4ZWGA 4TO3A 2O6IA 1YNBA 5AO2A 4X9EA 3TMDA 4QQYA 4XDSA 5TK6A 4L1JB 4TO1A 2HEKA 4QG1A 5AO4A 4TNZA 3HC1A 2CQZA 5AO0A 1VQRA 3MEMA 4BZCA 1VJ7A 4Q2DA 4BZBA 4QFYA 4Q7HA 3HI0A 4TNQA 2Q14A 5AO3A 2PAQA 3P3QA 4MLMA 4ME4A 4TNPA 3CCGA 3IRHA 3RF0A 4RXRA 4MZ7A 4L7WA 3TM8A 1XX7A 5AO1A 4QFZA 2DQBA 2FLOA 3SK9A 1U6ZA 5TKAA 3I7AA 4L1JA 3GW7A 4TNYA 4DMBA 3KQ5A 2PARA 4N6WA 3NQWA 4TO0A 3KH1A 4TO6A 4RXOA 4MCWA 5TK9A 4L7EA 4MLNA 4QQWA 5TK8A 2GZ4A 4TO5A 4QQZA 3TMCA 4R8ZA 3MZOA 4TNXA 4QG2A 2PGSA 4RXQA 4RXPA 4ZWEA 3M1TA 4QFXA 3S4LA 3TMBA 5TK7A 4N71A 2PAUA
chains in the Genus database with same CATH homology


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