SMTL ID : 3g5i.1

Crystal Structure of the E.coli RihA pyrimidine nucleosidase bound to a iminoribitol-based inhibitor

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-tetramer

Ligands

1 x BME: BETA-MERCAPTOETHANOL(Non-functional Binders)

BME.1: 4 residues within 4Å: Chain A: Q.101, C.103, L.108, K.111 No protein-ligand interaction detected (PLIP)

4 x CA: CALCIUM ION(Non-covalent)

CA.2: 6 residues within 4Å: Chain A: D.11, D.16, N.40, T.125, D.242 Ligands: DNB.3 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.11, A:D.16, A:D.16, A:T.125, H2O.1 CA.4: 6 residues within 4Å: Chain B: D.11, D.16, N.40, T.125, D.242 Ligands: DNB.5 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.11, B:D.16, B:D.16, B:T.125, H2O.6 CA.6: 6 residues within 4Å: Chain C: D.11, D.16, N.40, T.125, D.242 Ligands: DNB.7 5 PLIP interactions: 4 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.11, C:D.16, C:T.125, C:D.242, H2O.13 CA.8: 6 residues within 4Å: Chain D: D.11, D.16, N.40, T.125, D.242 Ligands: DNB.9 5 PLIP interactions: 4 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:D.11, D:D.16, D:D.16, D:T.125, H2O.15

4 x DNB: (2S,3S,4R,5R)-2-(3,4-diaminophenyl)-5-(hydroxymethyl)pyrrolidine-3,4-diol(Non-covalent)

DNB.3: 15 residues within 4Å: Chain A: D.15, D.16, N.40, A.79, V.82, H.83, T.125, M.151, N.159, E.165, F.166, N.167, H.241, D.242 Ligands: CA.2 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:A.79, A:V.82, A:F.166 Hydrogen bonds: A:N.40, A:N.159, A:N.159, A:N.167, A:N.167, A:H.241, A:D.242, A:D.242 pi-Stacking: A:H.83 DNB.5: 13 residues within 4Å: Chain B: D.15, D.16, N.40, T.125, M.151, N.159, W.160, E.165, F.166, N.167, H.241, D.242 Ligands: CA.4 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:N.40, B:N.159, B:N.159, B:E.165, B:N.167, B:N.167, B:D.242 DNB.7: 11 residues within 4Å: Chain C: D.15, D.16, N.40, T.125, M.151, N.159, E.165, F.166, N.167, D.242 Ligands: CA.6 8 PLIP interactions: 8 interactions with chain C Hydrophobic interactions: C:F.166 Hydrogen bonds: C:D.15, C:N.40, C:N.159, C:N.159, C:N.167, C:N.167, C:D.242 DNB.9: 13 residues within 4Å: Chain D: D.15, D.16, N.40, T.125, M.151, N.159, W.160, E.165, F.166, N.167, H.241, D.242 Ligands: CA.8 9 PLIP interactions: 9 interactions with chain D Hydrophobic interactions: D:F.166 Hydrogen bonds: D:N.40, D:N.159, D:N.159, D:E.165, D:N.167, D:N.167, D:D.242, D:D.242

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Garau, G. et al., Active site plasticity revealed from the structure of the enterobacterial N-ribohydrolase RihA bound to a competitive inhibitor. Bmc Struct.Biol. (2010)

Release Date

2010-02-09

Peptides

Pyrimidine-specific ribonucleoside hydrolase rihA: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Pyrimidine-specific ribonucleoside hydrolase rihA