SMTL ID : 3ixq.1

Structure of ribose 5-phosphate isomerase a from methanocaldococcus jannaschii

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.78 Å

Oligo State

homo-tetramer

Ligands

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

CL.1: 6 residues within 4Å: Chain A: G.98, G.100, G.101, C.102, E.106 Ligands: PGO.4 Ligand excluded by PLIP CL.5: 6 residues within 4Å: Chain B: G.98, G.100, G.101, C.102, E.106 Ligands: PGO.6 Ligand excluded by PLIP CL.9: 6 residues within 4Å: Chain C: G.98, G.100, G.101, C.102, E.106 Ligands: PGO.10 Ligand excluded by PLIP CL.13: 6 residues within 4Å: Chain D: G.98, G.100, G.101, C.102, E.106 Ligands: PGO.15 Ligand excluded by PLIP

11 x PGO: S-1,2-PROPANEDIOL(Non-covalent)

PGO.2: 5 residues within 4Å: Chain A: A.33, L.34, R.37, L.62, Y.66 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:L.34 Hydrogen bonds: A:R.37, A:Y.66 PGO.3: 7 residues within 4Å: Chain A: K.7, G.29, S.30, T.31, K.124 Chain B: R.167 Ligands: PGO.4 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.30, A:T.31, A:T.31 Water bridges: A:G.29, A:A.32 PGO.4: 10 residues within 4Å: Chain A: T.28, D.83, G.84, A.85, D.86, K.97, G.98, E.106 Ligands: CL.1, PGO.3 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:D.86, A:D.86, A:G.98 Water bridges: A:T.31, A:G.100 PGO.6: 10 residues within 4Å: Chain B: G.84, A.85, D.86, K.97, G.98, G.99, G.100, E.106 Ligands: CL.5, PGO.8 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:K.97, B:G.98, B:G.100 Water bridges: B:K.97 PGO.7: 5 residues within 4Å: Chain B: L.70, V.71 Chain D: F.51, L.70, V.71 6 PLIP interactions: 3 interactions with chain D, 3 interactions with chain B Hydrophobic interactions: D:F.51 Hydrogen bonds: D:L.70, B:L.70, B:L.70 Water bridges: D:L.70, B:E.75 PGO.8: 7 residues within 4Å: Chain A: R.167 Chain B: K.7, G.29, S.30, T.31, K.124 Ligands: PGO.6 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:S.30, B:T.31, B:K.124 Water bridges: B:T.28, B:G.29, B:A.85 PGO.10: 10 residues within 4Å: Chain C: T.28, D.83, G.84, A.85, D.86, K.97, G.98, E.106 Ligands: CL.9, PGO.11 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:D.86, C:G.98 Water bridges: C:T.31 PGO.11: 4 residues within 4Å: Chain C: G.29, S.30, T.31 Ligands: PGO.10 7 PLIP interactions: 7 interactions with chain C Hydrogen bonds: C:S.30, C:S.30, C:T.31, C:T.31 Water bridges: C:T.31, C:T.31, C:A.85 PGO.14: 6 residues within 4Å: Chain D: K.7, G.29, S.30, T.31, K.124 Ligands: PGO.15 6 PLIP interactions: 6 interactions with chain D Hydrogen bonds: D:S.30, D:T.31, D:K.124 Water bridges: D:T.28, D:G.29, D:A.85 PGO.15: 11 residues within 4Å: Chain D: T.28, G.29, D.83, G.84, A.85, D.86, K.97, G.98, E.106 Ligands: CL.13, PGO.14 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:G.84, D:K.97, D:G.98 PGO.16: 6 residues within 4Å: Chain C: E.58 Chain D: L.162, G.163, K.166, R.167, G.168 5 PLIP interactions: 4 interactions with chain D, 1 interactions with chain C Hydrophobic interactions: D:L.162 Hydrogen bonds: D:G.163, D:G.168, D:G.168, C:E.58

1 x ACT: ACETATE ION(Non-functional Binders)

ACT.12: 2 residues within 4Å: Chain C: P.54, S.56 1 PLIP interactions: 1 interactions with chain C Water bridges: C:Q.105

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Strange, R.W. et al., The structure of an archaeal ribose-5-phosphate isomerase from Methanocaldococcus jannaschii (MJ1603). Acta Crystallogr.,Sect.F (2009)

Release Date

2009-10-06

Peptides

Ribose-5-phosphate isomerase A: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Ribose-5-phosphate isomerase A