SMTL ID : 3cf8.1

Crystal structure of (3R)-Hydroxyacyl-Acyl Carrier Protein Dehydratase (FabZ) from Helicobacter pylori in complex with quercetin

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

homo-hexamer

Ligands

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

CL.1: 4 residues within 4Å: Chain A: H.58, P.66, G.67 Ligands: QUE.5 Ligand excluded by PLIP CL.6: 3 residues within 4Å: Chain B: H.58, P.66, G.67 Ligand excluded by PLIP CL.9: 3 residues within 4Å: Chain C: H.58, G.67 Chain D: F.101 Ligand excluded by PLIP CL.12: 3 residues within 4Å: Chain D: H.58, P.66, G.67 Ligand excluded by PLIP CL.13: 3 residues within 4Å: Chain E: H.58, G.67 Chain F: F.101 Ligand excluded by PLIP CL.14: 3 residues within 4Å: Chain E: F.101 Chain F: H.58, G.67 Ligand excluded by PLIP

6 x BEN: BENZAMIDINE(Non-functional Binders)

BEN.2: 4 residues within 4Å: Chain A: Q.40, E.124, V.125, L.126 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:E.124, A:L.126 Hydrogen bonds: A:Q.40, A:E.124 BEN.3: 3 residues within 4Å: Chain A: G.137, T.138, E.148 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:T.138, A:E.148 Water bridges: A:E.124, A:G.136, A:G.137, A:G.137 BEN.4: 4 residues within 4Å: Chain A: M.131, I.132, M.154, I.155 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:M.131, A:I.132 BEN.7: 2 residues within 4Å: Chain B: W.87, G.88 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:W.87 Water bridges: B:D.90 BEN.8: 8 residues within 4Å: Chain B: I.20, L.21, P.22, H.23, F.83, A.94, K.97, V.99 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:I.20, B:L.21, B:P.22, B:F.83, B:V.99 Hydrogen bonds: B:V.99 Water bridges: B:H.23, B:V.99, B:V.99 BEN.10: 6 residues within 4Å: Chain C: A.38, T.84, S.85, L.86, W.87, G.88 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:T.84

2 x QUE: 3,5,7,3',4'-PENTAHYDROXYFLAVONE(Non-covalent)

QUE.5: 12 residues within 4Å: Chain A: F.59, K.62, I.64, F.109, R.110, I.111, P.112 Chain B: I.98, V.99, Y.100, R.158 Ligands: CL.1 11 PLIP interactions: 5 interactions with chain A, 6 interactions with chain B Hydrophobic interactions: A:F.59, A:K.62, A:I.64, A:P.112, B:I.98, B:I.98, B:I.98, B:Y.100 Hydrogen bonds: A:I.111, B:Y.100, B:R.158 QUE.11: 13 residues within 4Å: Chain C: I.20, L.21, P.22, H.23, G.79, F.83, A.94, K.97, I.98, V.99, Y.100 Chain D: F.59, I.64 7 PLIP interactions: 1 interactions with chain D, 6 interactions with chain C pi-Stacking: D:F.59 Hydrophobic interactions: C:L.21, C:P.22, C:I.98, C:I.98, C:V.99 Hydrogen bonds: C:H.23

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhang, L. et al., Three flavonoids targeting the beta-hydroxyacyl-acyl carrier protein dehydratase from Helicobacter pylori: crystal structure characterization with enzymatic inhibition assay. Protein Sci. (2008)

Release Date

2008-12-09

Peptides

(3R)-hydroxymyristoyl-acyl carrier protein dehydratase: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

(3R)-hydroxymyristoyl-acyl carrier protein dehydratase

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