4R8ZA

Crystal structure of pa4781 hd-gyp domain from pseudomonas aeruginosa at 2.2a resolution showing a bi-metallic ni ion center
Total Genus 85

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
85
sequence length
218
structure length
218
Chain Sequence
RTRQLQQLQDAVIEALATLGDLRDNPRSRHLPRIERYVRLLAEHLAAQRAFADELTPEAVDLLSKSALLHDIGKVAVPDRVLLNPGQLDAADTALLQGHTRAGRDALASAERRLGQPSGFLRFARQIAYSHHERWDGRGFPEGLAGERIPLAARIVALADRYDELTSRHAYRPPLAHAEAVLLIQAGAGSEFDPRLVEAFVAVADAFAEVARRYADSA

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
AH1 (152-170)AH2 (179-197)TIV2 (175-178)TI2 (172-175)TI1 (171-174)TIV1 (173-176)AH3 (199-203)EMPTYAH4 (207-218)TIV3 (203-206)Updating...
connected with : NaN
molecule tags Hydrolase
source organism Pseudomonas aeruginosa pao1
publication title Structural basis of functional diversification of the HD-GYP domain revealed by the Pseudomonas aeruginosa PA4781 protein, which displays an unselective bimetallic binding site.
pubmed doi rcsb
molecule keywords Cyclic di-GMP phosphodiesterase
total genus 85
structure length 218
sequence length 218
chains with identical sequence B
ec nomenclature ec 3.1.4.1: Phosphodiesterase I.
pdb deposition date 2014-09-03

pfam database annotations

chain Pfam Accession Code Pfam Family Identifier Pfam Description
A PF13487 HD_5 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 4r8zA00
2PQ7A 4ZWEA 4Q7HA 5AO1A 4RXSA 3KH1A 3I7AA 4LRLA 3TMBA 2PAQA 5TK7A 4QFYA 2OGIA 4RXQA 1XX7A 4TNRA 1YOYA 4ME4A 5TK8A 4RXRA 3NQWA 3MZOA 2DQBA 3TMDA 4BZBA 3CCGA 4X9EA 4TO0A 4MCWA 1VJ7A 4ZWGA 4TNXA 4QG0A 3RF0A 4N6WA 4TO3A 4TNYA 4MLNA 2O6IA 4TNQA 2PAUA 2PGSA 4QG4A 4L1JB 2O08A 4TO5A 1VQRA 4QG1A 4TO2A 2CQZA 5AO2A 3MEMA 3U1NA 5TKAA 3NR1A 1U6ZA 3TM8A 2FLOA 3HC1A 4TNPA 4TO4A 4QFXA 2HEKA 4MZ7A 4TNZA 4R8ZA 2Q14A 3TMCA 4TO6A 2GZ4A 5AO3A 4L7EA 4BZCA 4L7WA 1YNBA 3HI0A 3IRHA 3P3QA 3BG2A 4DMBA 4QFZA 4L1JA 4MLMA 5TK9A 2PARA 4RXPA 4QG2A 4N71A 5AO0A 4MDZA 3M1TA 3LJXA 5TK6A 4TO1A 4XDSA 4RXOA 5AO4A
chains in the Genus database with same CATH superfamily
2PQ7A 4ZWEA 4Q7HA 4Q2CA 4RXSA 5AO1A 3KH1A 3I7AA 4LRLA 3TMBA 2PAQA 5TK7A 3S4LA 4QFYA 2OGIA 4RXQA 4Q2DA 1XX7A 4TNRA 1YOYA 4ME4A 5TK8A 3SKDA 4RXRA 3NQWA 3MZOA 2DQBA 3TMDA 4BZBA 3CCGA 4X9EA 4TO0A 4MCWA 1VJ7A 4ZWGA 4TNXA 4QG0A 3RF0A 4N6WA 4TO3A 4TNYA 4MLNA 2O6IA 4TNQA 2PAUA 2PGSA 4QG4A 4L1JB 2O08A 4QQWA 4TO5A 1VQRA 3KQ5A 4QG1A 4TO2A 2CQZA 5AO2A 3MEMA 3U1NA 5TKAA 3NR1A 1U6ZA 3TM8A 2FLOA 3HC1A 4TNPA 4QQYA 4TO4A 4QFXA 2HEKA 3SK9A 4MZ7A 4TNZA 4R8ZA 2Q14A 3TMCA 4TO6A 2GZ4A 5AO3A 4L7EA 4BZCA 4L7WA 1YNBA 4QQXA 3HI0A 3IRHA 3P3QA 3BG2A 4DMBA 4QFZA 4L1JA 4MLMA 5TK9A 2PARA 4RXPA 4QG2A 4N71A 4QQZA 5AO0A 4MDZA 3M1TA 3GW7A 3LJXA 5TK6A 4TO1A 4XDSA 4RXOA 5AO4A
chains in the Genus database with same CATH topology
2PQ7A 4ZWEA 4Q7HA 4Q2CA 4RXSA 5AO1A 3KH1A 3I7AA 4LRLA 3TMBA 2PAQA 5TK7A 3S4LA 4QFYA 2OGIA 4RXQA 4Q2DA 1XX7A 4TNRA 1YOYA 4ME4A 5TK8A 3SKDA 4RXRA 3NQWA 3MZOA 2DQBA 3TMDA 4BZBA 3CCGA 4X9EA 4TO0A 4MCWA 1VJ7A 4ZWGA 4TNXA 4QG0A 3RF0A 4N6WA 4TO3A 4TNYA 4MLNA 2O6IA 4TNQA 2PAUA 2PGSA 4QG4A 4L1JB 2O08A 4QQWA 4TO5A 1VQRA 3KQ5A 4QG1A 4TO2A 2CQZA 5AO2A 3MEMA 3U1NA 5TKAA 3NR1A 1U6ZA 3TM8A 2FLOA 3HC1A 4TNPA 4QQYA 4TO4A 4QFXA 2HEKA 3SK9A 4MZ7A 4TNZA 4R8ZA 2Q14A 3TMCA 4TO6A 2GZ4A 5AO3A 4L7EA 4BZCA 4L7WA 1YNBA 4QQXA 3HI0A 3IRHA 3P3QA 3BG2A 4DMBA 4QFZA 4L1JA 4MLMA 5TK9A 2PARA 4RXPA 4QG2A 4N71A 4QQZA 5AO0A 4MDZA 3M1TA 3GW7A 3LJXA 5TK6A 4TO1A 4XDSA 4RXOA 5AO4A
chains in the Genus database with same CATH homology


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