2PARA

Crystal structure of the 5'-deoxynucleotidase yfbr mutant e72a complexed with co(2+) and tmp
Total Genus 60
Loading diagram...

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
60
sequence length
186
structure length
175
Chain Sequence
KQSHFFAHLSRLKLINRWPLMRNVRTENVSEHSLQVAMVAHALAAIKNRKFGGNVNAERIALLAMYHDASAVLTGDLPTEYKAIEKIAQQKLVDMVPEELRDIFAPLIDEHAYSDEEKSLVKQADALCAYLKCLEELAAGNNEFLLAKTRLEATLEARRSQEMDYFMEIFVPSFH
Loading diagram...

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
{{ tooltip.sname }} connected with {{ tooltip.tname }} : {{qFormat(tooltip.svalue) }}
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 60
structure length 175
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 2parA00
4TO1A 2PARA 4ZWEA 4Q7HA 2PAUA 4RXOA 4X9EA 3RF0A 4L7EA 4RXQA 4N6WA 4R8ZA 2GZ4A 5AO3A 4TNZA 3HC1A 3KH1A 3TMDA 4TO0A 3BG2A 4MDZA 4TO4A 3IRHA 5TK6A 4TO2A 4DMBA 4XDSA 3U1NA 3NQWA 3CCGA 4QG0A 4QFZA 4TNXA 4TNPA 4QFYA 4BZBA 1YNBA 4TNRA 4TO5A 5AO4A 4RXPA 4RXRA 5TKAA 5TK9A 2PAQA 2CQZA 1VJ7A 4MZ7A 4QFXA 4QG2A 5AO1A 4MLMA 4L1JB 5AO2A 4TO3A 1U6ZA 3TMCA 4TNQA 3MZOA 1VQRA 1XX7A 3NR1A 2OGIA 2O6IA 1YOYA 4N71A 2PQ7A 4QG4A 3MEMA 5AO0A 3TM8A 3LJXA 3P3QA 4ZWGA 3TMBA 4ME4A 2DQBA 4MLNA 4MCWA 4L1JA 2O08A 5TK8A 4L7WA 4TO6A 5TK7A 4QG1A 4RXSA 2HEKA 4LRLA 3HI0A 3M1TA 4BZCA 2Q14A 3I7AA 2FLOA 4TNYA 2PGSA
chains in the Genus database with same CATH superfamily
4QQWA 4TO1A 4QQYA 3GW7A 2PARA 3SKDA 4QQXA 4ZWEA 4Q7HA 2PAUA 4RXOA 4X9EA 3RF0A 4L7EA 4RXQA 4N6WA 4R8ZA 2GZ4A 5AO3A 4TNZA 3HC1A 3KH1A 3TMDA 4TO0A 3BG2A 4MDZA 4TO4A 3IRHA 5TK6A 4Q2CA 4TO2A 4DMBA 4XDSA 3U1NA 3NQWA 3CCGA 4QG0A 4QFZA 4TNXA 4TNPA 4QFYA 4BZBA 1YNBA 4TNRA 4TO5A 5AO4A 3KQ5A 4RXPA 4RXRA 5TKAA 5TK9A 2PAQA 2CQZA 1VJ7A 4MZ7A 4QFXA 4QG2A 4QQZA 5AO1A 4MLMA 4L1JB 5AO2A 4TO3A 1U6ZA 3TMCA 4TNQA 3MZOA 1VQRA 1XX7A 3NR1A 2OGIA 4Q2DA 2O6IA 1YOYA 4N71A 2PQ7A 4QG4A 3MEMA 5AO0A 3TM8A 3LJXA 3P3QA 4ZWGA 3TMBA 4ME4A 2DQBA 4MLNA 4MCWA 4L1JA 2O08A 5TK8A 4L7WA 4TO6A 5TK7A 4QG1A 4RXSA 3SK9A 2HEKA 4LRLA 3HI0A 3M1TA 4BZCA 2Q14A 3S4LA 3I7AA 2FLOA 4TNYA 2PGSA
chains in the Genus database with same CATH topology
4QQWA 4TO1A 4QQYA 3GW7A 2PARA 3SKDA 4QQXA 4ZWEA 4Q7HA 2PAUA 4RXOA 4X9EA 3RF0A 4L7EA 4RXQA 4N6WA 4R8ZA 2GZ4A 5AO3A 4TNZA 3HC1A 3KH1A 3TMDA 4TO0A 3BG2A 4MDZA 4TO4A 3IRHA 5TK6A 4Q2CA 4TO2A 4DMBA 4XDSA 3U1NA 3NQWA 3CCGA 4QG0A 4QFZA 4TNXA 4TNPA 4QFYA 4BZBA 1YNBA 4TNRA 4TO5A 5AO4A 3KQ5A 4RXPA 4RXRA 5TKAA 5TK9A 2PAQA 2CQZA 1VJ7A 4MZ7A 4QFXA 4QG2A 4QQZA 5AO1A 4MLMA 4L1JB 5AO2A 4TO3A 1U6ZA 3TMCA 4TNQA 3MZOA 1VQRA 1XX7A 3NR1A 2OGIA 4Q2DA 2O6IA 1YOYA 4N71A 2PQ7A 4QG4A 3MEMA 5AO0A 3TM8A 3LJXA 3P3QA 4ZWGA 3TMBA 4ME4A 2DQBA 4MLNA 4MCWA 4L1JA 2O08A 5TK8A 4L7WA 4TO6A 5TK7A 4QG1A 4RXSA 3SK9A 2HEKA 4LRLA 3HI0A 3M1TA 4BZCA 2Q14A 3S4LA 3I7AA 2FLOA 4TNYA 2PGSA
chains in the Genus database with same CATH homology


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

 
#similar chains in the Genus database (?% sequence similarity)
...loading similar chains, please wait...
#similar chains, but unknotted
...loading similar chains, please wait...
#similar chains in the pdb database (?% sequence similarity)
...loading similar chains, please wait...