SMTL ID : 4p6p.1

Structure of ribB complexed with inhibitor (4PEH) and metal ions

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.86 Å

Oligo State

homo-dimer

Ligands

2 x RES: 4-PHOSPHO-D-ERYTHRONOHYDROXAMIC ACID(Non-covalent)

RES.1: 17 residues within 4Å: Chain A: R.57, E.58, D.62, C.87, N.111, T.113, F.115, L.160, R.170, G.172, H.173, T.174, L.192, E.194 Chain B: H.156 Ligands: ZN.2, ZN.3 7 PLIP interactions: 6 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:H.173, A:T.174, A:T.174, B:H.156 Water bridges: A:E.194 Salt bridges: A:R.57, A:R.170 RES.5: 17 residues within 4Å: Chain A: H.156 Chain B: R.57, E.58, D.62, C.87, N.111, T.113, F.115, L.160, R.170, G.172, H.173, T.174, L.192, E.194 Ligands: ZN.6, ZN.7 11 PLIP interactions: 10 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:H.173, B:T.174, B:E.194, A:H.156 Water bridges: B:I.85, B:N.111, B:N.111, B:T.174, B:E.194 Salt bridges: B:R.57, B:R.170

11 x ZN: ZINC ION(Non-covalent)

ZN.2: 5 residues within 4Å: Chain A: E.58, D.62, H.173 Ligands: RES.1, ZN.3 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.58, A:H.173, H2O.3 ZN.3: 3 residues within 4Å: Chain A: E.58 Ligands: RES.1, ZN.2 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:E.58, H2O.3, H2O.4, H2O.14 ZN.4: 2 residues within 4Å: Chain A: D.96, R.161 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.96, A:D.96, H2O.2 ZN.6: 5 residues within 4Å: Chain B: E.58, D.62, H.173 Ligands: RES.5, ZN.7 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.58, B:H.173, H2O.11 ZN.7: 3 residues within 4Å: Chain B: E.58 Ligands: RES.5, ZN.6 4 PLIP interactions: 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:E.58, H2O.3, H2O.12, H2O.12 ZN.8: 4 residues within 4Å: Chain B: E.37, F.232 Ligands: ZN.9, ZN.10 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:E.37, B:E.37 ZN.9: 4 residues within 4Å: Chain B: E.37, F.232 Ligands: ZN.8, ZN.10 No protein-ligand interaction detected (PLIP) ZN.10: 4 residues within 4Å: Chain B: E.37, F.232 Ligands: ZN.8, ZN.9 No protein-ligand interaction detected (PLIP) ZN.11: 1 residues within 4Å: Chain B: D.233 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.233, B:D.233, H2O.10, H2O.10 ZN.12: 3 residues within 4Å: Chain B: E.81, F.211, H.215 2 PLIP interactions: 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.215, H2O.11 ZN.13: 1 residues within 4Å: Chain B: E.210 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.210, B:E.210, H2O.9, H2O.11

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Islam, Z. et al., Structural Basis for Competitive Inhibition of 3,4-Dihydroxy-2-butanone-4-phosphate Synthase from Vibrio cholerae. J.Biol.Chem. (2015)

Release Date

2015-03-25

Peptides

3,4-dihydroxy-2-butanone 4-phosphate synthase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

3,4-dihydroxy-2-butanone 4-phosphate synthase

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