SMTL ID : 4wr2.1

Crystal structure of a putative pyrimidine-specific ribonucleoside hydrolase (RihA) Protein from Shewanella loihica PV-4 (SHEW_0697, Target PSI-029635) with divalent cation and PEG 400 bound at the active site

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

homo-tetramer

Ligands

4 x CA: CALCIUM ION(Non-covalent)

CA.1: 4 residues within 4Å: Chain A: D.34, D.39, S.148, D.265 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.39, A:D.39, A:S.148, H2O.7, H2O.10 CA.3: 4 residues within 4Å: Chain B: D.34, D.39, S.148, D.265 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.39, B:D.39, B:S.148, H2O.18, H2O.21 CA.5: 4 residues within 4Å: Chain C: D.34, D.39, S.148, D.265 5 PLIP interactions: 3 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:D.39, C:D.39, C:S.148, H2O.29, H2O.32 CA.7: 4 residues within 4Å: Chain D: D.34, D.39, S.148, D.265 5 PLIP interactions: 3 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:D.39, D:D.39, D:S.148, H2O.40, H2O.43

4 x 1PE: PENTAETHYLENE GLYCOL(Non-functional Binders)

1PE.2: 8 residues within 4Å: Chain A: N.63, V.180, N.182, W.183, L.213, W.256, F.258, H.264 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.63, A:N.182 Water bridges: A:V.180, A:V.180 1PE.4: 8 residues within 4Å: Chain B: N.63, V.180, N.182, W.183, L.213, W.256, F.258, H.264 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:N.63, B:N.182 Water bridges: B:V.180, B:V.180 1PE.6: 8 residues within 4Å: Chain C: N.63, V.180, N.182, W.183, L.213, W.256, F.258, H.264 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:N.63, C:N.182 Water bridges: C:V.180, C:V.180 1PE.8: 8 residues within 4Å: Chain D: N.63, V.180, N.182, W.183, L.213, W.256, F.258, H.264 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:N.63, D:N.182 Water bridges: D:V.180, D:V.180

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Himmel, D.M. et al., Crystal structure of a putative pyrimidine-specific ribonucleoside hydrolase (RihA) Protein from Shewanella loihica PV-4 (SHEW_0697, Target PSI-029635) with divalent cation and PEG 400 bound at the active site. To be published

Release Date

2014-11-12

Peptides

Pyrimidine-specific ribonucleoside hydrolase RihA: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

Pyrimidine-specific ribonucleoside hydrolase RihA