SMTL ID : 3b9x.1

Crystal structure of the E. coli pyrimidine nucleoside hydrolase YeiK in complex with inosine

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-tetramer

Ligands

4 x CA: CALCIUM ION(Non-covalent)

CA.1: 6 residues within 4Å: Chain A: D.31, D.36, N.60, V.144, D.260 Ligands: NOS.2 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.31, A:D.36, A:V.144, A:D.260, H2O.4 CA.3: 6 residues within 4Å: Chain B: D.31, D.36, N.60, V.144, D.260 Ligands: NOS.4 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.31, B:D.36, B:D.36, B:D.260, H2O.4 CA.5: 6 residues within 4Å: Chain C: D.31, D.36, N.60, V.144, D.260 Ligands: NOS.6 5 PLIP interactions: 4 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.31, C:D.36, C:D.36, C:D.260, H2O.9 CA.7: 6 residues within 4Å: Chain D: D.31, D.36, N.60, V.144, D.260 Ligands: NOS.8 5 PLIP interactions: 4 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:D.31, D:D.36, D:V.144, D:D.260, H2O.11

4 x NOS: INOSINE(Non-covalent)

NOS.2: 17 residues within 4Å: Chain A: D.31, D.35, D.36, N.60, I.101, H.102, V.144, M.170, N.178, E.184, F.185, N.186, Q.247, Y.251, H.259, D.260 Ligands: CA.1 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:N.60, A:N.178, A:E.184, A:N.186, A:Q.247, A:Y.251 pi-Cation interactions: A:H.102 NOS.4: 14 residues within 4Å: Chain B: D.35, D.36, N.60, V.144, M.170, N.178, E.184, F.185, N.186, Q.247, Y.251, H.259, D.260 Ligands: CA.3 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:N.60, B:N.60, B:N.178, B:N.178, B:N.186, B:Q.247, B:Y.251, B:Y.251 NOS.6: 13 residues within 4Å: Chain C: D.35, D.36, N.60, A.98, V.144, M.170, N.178, E.184, F.185, N.186, H.259, D.260 Ligands: CA.5 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:N.60, C:N.60, C:N.178, C:N.178, C:E.184, C:N.186 NOS.8: 19 residues within 4Å: Chain D: D.35, D.36, N.60, A.98, I.101, H.102, V.144, M.170, N.178, F.179, E.184, F.185, N.186, L.209, Q.247, Y.251, H.259, D.260 Ligands: CA.7 8 PLIP interactions: 8 interactions with chain D Hydrogen bonds: D:N.60, D:N.178, D:F.185, D:N.186, D:Q.247, D:Y.251, D:Y.251 pi-Stacking: D:H.102

1 x TAM: TRIS(HYDROXYETHYL)AMINOMETHANE(Non-covalent)

TAM.9: 9 residues within 4Å: Chain C: M.156, Q.157, P.158 Chain D: L.63, L.67, A.85, G.86, P.88, H.123 4 PLIP interactions: 2 interactions with chain D, 2 interactions with chain C Hydrophobic interactions: D:L.63 Water bridges: D:H.123, C:Q.157 Hydrogen bonds: C:M.156

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Iovane, E. et al., Structural basis for substrate specificity in group I nucleoside hydrolases. Biochemistry (2008)

Release Date

2008-04-01

Peptides

Pyrimidine-specific ribonucleoside hydrolase rihB: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Pyrimidine-specific ribonucleoside hydrolase rihB