SMTL ID : 3clh.1

Crystal structure of 3-dehydroquinate synthase (DHQS)from Helicobacter pylori

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

homo-dimer

Ligands

2 x ZN: ZINC ION(Non-covalent)

ZN.1: 2 residues within 4Å: Chain A: H.248 Ligands: NAD.2 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.248, H2O.4 ZN.3: 4 residues within 4Å: Chain B: E.174, H.231, H.248 Ligands: NAD.4 No protein-ligand interaction detected (PLIP)

2 x NAD: NICOTINAMIDE-ADENINE-DINUCLEOTIDE(Non-covalent)

NAD.2: 25 residues within 4Å: Chain A: D.34, I.36, V.37, L.40, H.41, S.61, G.62, E.63, K.66, G.94, G.95, V.96, D.99, T.119, T.120, L.122, D.126, A.127, K.132, N.142, F.159, T.162, L.163, E.167 Ligands: ZN.1 20 PLIP interactions: 20 interactions with chain A Hydrophobic interactions: A:L.122, A:A.127 Hydrogen bonds: A:S.61, A:S.61, A:E.63, A:K.66, A:G.95, A:V.96, A:D.99, A:T.119, A:N.142 Water bridges: A:G.62, A:K.66, A:G.94, A:G.94, A:T.120, A:D.126, A:K.132, A:N.136, A:E.167 NAD.4: 24 residues within 4Å: Chain B: D.34, I.36, V.37, L.40, H.41, S.61, E.63, K.66, G.94, G.95, V.96, D.99, T.119, T.120, L.122, D.126, A.127, K.132, N.142, F.159, T.162, L.163, E.167 Ligands: ZN.3 16 PLIP interactions: 16 interactions with chain B Hydrogen bonds: B:S.61, B:S.61, B:E.63, B:K.66, B:G.94, B:G.95, B:V.96, B:T.119, B:T.119, B:T.120, B:K.132, B:N.142, B:T.162 Water bridges: B:D.99, B:K.132, B:K.210

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Liu, J.S. et al., Structure-based inhibitor discovery of Helicobacter pylori dehydroquinate synthase. Biochem.Biophys.Res.Commun. (2008)

Release Date

2009-03-24

Peptides

3-dehydroquinate synthase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

3-dehydroquinate synthase