SMTL ID : 3b7j.1

Crystal structure of (3R)-Hydroxyacyl-Acyl Carrier Protein Dehydratase(FabZ) from Helicobacter pylori complexed with juglone

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: 3 residues within 4Å: Chain A: H.58, P.66, G.67 Ligand excluded by PLIP CL.3: 3 residues within 4Å: Chain B: H.58, P.66, G.67 Ligand excluded by PLIP CL.7: 3 residues within 4Å: Chain C: H.58, G.67 Chain D: F.101 Ligand excluded by PLIP CL.10: 3 residues within 4Å: Chain D: H.58, P.66, G.67 Ligand excluded by PLIP CL.11: 4 residues within 4Å: Chain E: H.58, P.66, 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

7 x BEN: BENZAMIDINE(Non-functional Binders)

BEN.2: 3 residues within 4Å: Chain A: Q.40, E.124, V.125 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:E.124 Hydrogen bonds: A:Q.40, A:E.124 Water bridges: A:Q.40 BEN.4: 10 residues within 4Å: Chain B: I.20, L.21, P.22, H.23, G.79, F.83, A.94, K.97, I.98, V.99 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:I.20, B:L.21, B:F.83, B:F.83, B:I.98, B:V.99 Hydrogen bonds: B:V.99 BEN.5: 2 residues within 4Å: Chain B: W.87, G.88 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:W.87 Water bridges: B:D.90, B:D.90 BEN.8: 6 residues within 4Å: Chain C: A.38, T.84, S.85, L.86, W.87, G.88 No protein-ligand interaction detected (PLIP) BEN.12: 4 residues within 4Å: Chain E: Q.40, E.124, V.125, L.126 4 PLIP interactions: 4 interactions with chain E Hydrophobic interactions: E:E.124, E:L.126 Hydrogen bonds: E:Q.40, E:E.124 BEN.13: 5 residues within 4Å: Chain E: L.126, G.136, G.137, A.149, E.150 2 PLIP interactions: 2 interactions with chain E Hydrophobic interactions: E:E.150 Hydrogen bonds: E:E.150 BEN.15: 3 residues within 4Å: Chain F: L.86, W.87, D.90 3 PLIP interactions: 3 interactions with chain F Hydrogen bonds: F:D.90, F:D.90 pi-Stacking: F:W.87

2 x JUG: 5-hydroxynaphthalene-1,4-dione(Non-covalent)

JUG.6: 6 residues within 4Å: Chain A: I.64, F.109, R.110, I.111, P.112 Chain B: Y.100 5 PLIP interactions: 2 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:Y.100, A:I.64, A:P.112 pi-Stacking: B:Y.100 Water bridges: A:I.111 JUG.9: 10 residues within 4Å: Chain C: I.20, L.21, P.22, H.23, G.79, A.94, K.97, I.98, V.99, R.158 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:P.22, C:V.99, C:V.99 Hydrogen bonds: C:V.99

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kong, Y.H. et al., Natural product juglone targets three key enzymes from Helicobacter pylori: inhibition assay with crystal structure characterization. ACTA PHARMACOL.SIN. (2008)

Release Date

2008-09-02

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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