SMTL ID : 5krv.1

1-deoxy-D-xylulose 5-phosphate reductoisomerase from Vibrio vulnificus in complex Arginine

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-dimer

Ligands

11 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.1: 5 residues within 4Å: Chain A: Y.311, P.312, R.314 Chain B: P.186, Y.287 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.314 Water bridges: A:Q.190 EDO.2: 8 residues within 4Å: Chain A: L.147, N.149, K.150, P.173, V.174, D.175, H.178, E.259 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:V.174, A:D.175, A:H.178 EDO.3: 6 residues within 4Å: Chain A: I.46, P.50, F.53, S.54, V.55, W.74 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:V.55, A:V.55 Water bridges: A:R.73 EDO.4: 1 residues within 4Å: Chain A: A.109 No protein-ligand interaction detected (PLIP) EDO.5: 3 residues within 4Å: Chain A: Q.72, R.73, Q.75 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.75 EDO.6: 4 residues within 4Å: Chain A: P.228, E.229, L.372, R.374 No protein-ligand interaction detected (PLIP) EDO.10: 8 residues within 4Å: Chain B: L.147, N.149, K.150, P.173, V.174, D.175, H.178, E.259 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:V.174, B:D.175 EDO.11: 2 residues within 4Å: Chain B: E.222, Q.230 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Q.230 EDO.12: 3 residues within 4Å: Chain B: F.337, A.344, E.348 No protein-ligand interaction detected (PLIP) EDO.13: 4 residues within 4Å: Chain B: T.35, D.61, S.62, N.63 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:T.35, B:D.61, B:S.62, B:N.63 EDO.14: 1 residues within 4Å: Chain B: A.109 No protein-ligand interaction detected (PLIP)

1 x ARG: ARGININE(Non-covalent)

ARG.7: 6 residues within 4Å: Chain A: D.61, A.82, N.83, K.84, G.106, Q.107 8 PLIP interactions: 6 interactions with chain A, 2 Ligand-Ligand interactions Hydrogen bonds: A:D.61, A:N.83, A:K.84, A:Q.107, R.7, R.7 Water bridges: A:K.84 Salt bridges: A:K.84

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

CL.8: 4 residues within 4Å: Chain A: G.210, S.211, N.252, K.253 Ligand excluded by PLIP

1 x SRT: S,R MESO-TARTARIC ACID(Non-covalent)

SRT.9: 4 residues within 4Å: Chain B: K.84, G.106, Q.107, E.108 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:Q.107, B:E.108 Salt bridges: B:K.84, B:K.84

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ussin, N.K. et al., Structural characterization of 1-deoxy-D-xylulose 5-phosphate Reductoisomerase from Vibrio vulnificus. Biochim Biophys Acta Proteins Proteom (2018)

Release Date

2017-07-12

Peptides

1-deoxy-D-xylulose 5-phosphate reductoisomerase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

1-deoxy-D-xylulose 5-phosphate reductoisomerase

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