SMTL ID : 3pfo.1

Crystal structure of a putative acetylornithine deacetylase (RPA2325) from RHODOPSEUDOMONAS PALUSTRIS CGA009 at 1.90 A resolution

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-dimer

Ligands

4 x ZN: ZINC ION(Non-covalent)

ZN.1: 6 residues within 4Å: Chain A: H.111, D.144, E.178, E.179, E.202 Ligands: ZN.2 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.111, A:D.144, A:E.202, A:E.202, H2O.1 ZN.2: 4 residues within 4Å: Chain A: D.144, E.179, H.402 Ligands: ZN.1 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.144, A:E.179, A:E.179, A:H.402, H2O.1 ZN.9: 4 residues within 4Å: Chain B: D.144, E.179, H.402 Ligands: ZN.10 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.144, B:E.179, B:E.179, B:H.402, H2O.17 ZN.10: 6 residues within 4Å: Chain B: H.111, D.144, E.178, E.179, E.202 Ligands: ZN.9 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.111, B:D.144, B:E.202, B:E.202, H2O.17

10 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.3: 6 residues within 4Å: Chain A: C.347, G.351, A.353, E.354, P.390 Ligands: EDO.5 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.351, A:E.354 Water bridges: A:V.352, A:V.352 EDO.4: 5 residues within 4Å: Chain A: N.257, A.258, V.269, K.270, N.271 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:V.269, A:N.271 EDO.5: 5 residues within 4Å: Chain A: S.384, G.388, I.389, P.390 Ligands: EDO.3 1 PLIP interactions: 1 interactions with chain A Water bridges: A:A.391 EDO.6: 4 residues within 4Å: Chain A: R.262, D.263, P.264, G.304 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.262, A:G.304 EDO.7: 4 residues within 4Å: Chain A: A.30, F.31, W.51, Q.55 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:A.30, A:Q.55 Water bridges: A:F.31, A:R.59 EDO.8: 9 residues within 4Å: Chain A: P.226, G.283, D.284, S.288, T.289, A.290, A.291, W.292 Chain B: H.402 6 PLIP interactions: 5 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:D.284, A:A.291, A:W.292, B:H.402 Water bridges: A:W.285, A:S.288 EDO.11: 4 residues within 4Å: Chain B: E.348, G.351, E.354, P.390 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:G.351, B:G.351, B:E.354 EDO.12: 1 residues within 4Å: Chain B: R.34 No protein-ligand interaction detected (PLIP) EDO.13: 3 residues within 4Å: Chain B: R.312, E.315, W.337 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.312, B:E.315 EDO.14: 4 residues within 4Å: Chain B: T.65, F.66, D.70, R.191 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:T.65, B:R.191, B:R.191

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Joint Center for Structural Genomics (JCSG), Crystal structure of a putative acetylornithine deacetylase (RPA2325) from RHODOPSEUDOMONAS PALUSTRIS CGA009 at 1.90 A resolution. To be published

Release Date

2010-11-10

Peptides

putative acetylornithine deacetylase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

putative acetylornithine deacetylase