SMTL ID : 1lk7.1

Structure of D-Ribose-5-Phosphate Isomerase from in complex with phospho-erythronic acid

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-tetramer

Ligands

10 x CL: CHLORIDE ION(Non-functional Binders)

CL.1: 6 residues within 4Å: Chain A: G.99, G.101, A.102, A.103, E.107 Ligands: DER.5 Ligand excluded by PLIP CL.2: 8 residues within 4Å: Chain A: S.57, Y.58, Q.59, D.174 Chain C: K.167, D.168, G.169, P.170 Ligand excluded by PLIP CL.3: 5 residues within 4Å: Chain A: V.165, N.166 Chain C: G.164, V.165, N.166 Ligand excluded by PLIP CL.6: 7 residues within 4Å: Chain B: G.99, G.101, A.102, A.103, L.104, E.107 Ligands: DER.9 Ligand excluded by PLIP CL.7: 8 residues within 4Å: Chain B: S.57, Y.58, Q.59, D.174 Chain D: K.167, D.168, G.169, P.170 Ligand excluded by PLIP CL.8: 6 residues within 4Å: Chain B: G.164, V.165, N.166 Chain D: G.164, V.165, N.166 Ligand excluded by PLIP CL.10: 6 residues within 4Å: Chain C: G.99, G.101, A.102, A.103, E.107 Ligands: DER.13 Ligand excluded by PLIP CL.11: 8 residues within 4Å: Chain A: K.167, D.168, G.169, P.170 Chain C: S.57, Y.58, Q.59, D.174 Ligand excluded by PLIP CL.14: 7 residues within 4Å: Chain D: G.99, G.101, A.102, A.103, L.104, E.107 Ligands: DER.16 Ligand excluded by PLIP CL.15: 8 residues within 4Å: Chain B: K.167, D.168, G.169, P.170 Chain D: S.57, Y.58, Q.59, D.174 Ligand excluded by PLIP

2 x NA: SODIUM ION(Non-functional Binders)

NA.4: 2 residues within 4Å: Chain A: N.175 Chain B: N.175 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.175 NA.12: 2 residues within 4Å: Chain C: N.175 Chain D: N.175 4 PLIP interactions: 2 interactions with chain C, 2 interactions with chain D Water bridges: C:N.177, C:N.177, D:N.177 Hydrogen bonds: D:N.175

4 x DER: D-4-PHOSPHOERYTHRONIC ACID(Non-covalent)

DER.5: 15 residues within 4Å: Chain A: T.28, G.29, S.30, T.31, D.85, G.86, A.87, D.88, K.98, G.99, R.100, G.101, E.107, K.125 Ligands: CL.1 18 PLIP interactions: 18 interactions with chain A Hydrogen bonds: A:S.30, A:T.31, A:T.31, A:G.86, A:D.88, A:G.99, A:G.101, A:E.107 Water bridges: A:S.30, A:T.32, A:T.32, A:A.87, A:R.100, A:R.100 Salt bridges: A:K.7, A:K.98, A:R.100, A:K.125 DER.9: 15 residues within 4Å: Chain B: T.28, G.29, S.30, T.31, D.85, G.86, A.87, D.88, K.98, G.99, R.100, G.101, E.107, K.125 Ligands: CL.6 14 PLIP interactions: 14 interactions with chain B Hydrogen bonds: B:S.30, B:T.31, B:T.31, B:D.85, B:G.86, B:G.99, B:R.100, B:G.101 Water bridges: B:G.29, B:T.32, B:A.87 Salt bridges: B:K.7, B:K.98, B:K.125 DER.13: 15 residues within 4Å: Chain C: T.28, G.29, S.30, T.31, D.85, G.86, A.87, D.88, K.98, G.99, R.100, G.101, E.107, K.125 Ligands: CL.10 21 PLIP interactions: 21 interactions with chain C Hydrogen bonds: C:S.30, C:T.31, C:G.86, C:D.88, C:G.99, C:G.101, C:E.107 Water bridges: C:K.7, C:S.30, C:T.32, C:T.32, C:A.87, C:R.100, C:R.100, C:R.100, C:K.125, C:K.125 Salt bridges: C:K.7, C:K.98, C:R.100, C:K.125 DER.16: 15 residues within 4Å: Chain D: T.28, G.29, S.30, T.31, D.85, G.86, A.87, D.88, K.98, G.99, R.100, G.101, E.107, K.125 Ligands: CL.14 18 PLIP interactions: 18 interactions with chain D Hydrogen bonds: D:S.30, D:T.31, D:T.31, D:G.86, D:D.88, D:G.99, D:G.101, D:E.107 Water bridges: D:G.29, D:S.30, D:T.32, D:A.87, D:A.87, D:D.88, D:K.125 Salt bridges: D:K.7, D:K.98, D:K.125

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ishikawa, K. et al., A Hyperthermostable D-Ribose-5-Phosphate Isomerase from Pyrococcus horikoshii Characterization and Three-Dimensional Structure. STRUCTURE (2002)

Release Date

2002-07-03

Peptides

D-Ribose-5-Phosphate Isomerase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

D-Ribose-5-Phosphate Isomerase

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