SMTL ID : 3ed0.1

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

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-hexamer

Ligands

7 x BEN: BENZAMIDINE(Non-functional Binders)

BEN.1: 3 residues within 4Å: Chain A: Q.40, E.124, V.125 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:E.124 Hydrogen bonds: A:Q.40, A:E.124 BEN.2: 3 residues within 4Å: Chain A: M.131, M.154, I.155 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:M.131 BEN.5: 9 residues within 4Å: Chain B: I.20, L.21, P.22, H.23, F.83, A.94, K.97, I.98, V.99 8 PLIP interactions: 8 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, B:V.99 BEN.6: 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.10: 2 residues within 4Å: Chain D: N.39, Q.40 1 PLIP interactions: 1 interactions with chain D Hydrophobic interactions: D:Q.40 BEN.12: 4 residues within 4Å: Chain E: E.124, V.125, L.126 Ligands: BEN.13 2 PLIP interactions: 2 interactions with chain E Hydrophobic interactions: E:L.126 Hydrogen bonds: E:E.124 BEN.13: 7 residues within 4Å: Chain E: K.106, L.126, G.136, G.137, A.149, E.150 Ligands: BEN.12 4 PLIP interactions: 4 interactions with chain E Hydrophobic interactions: E:L.126, E:E.150 Hydrogen bonds: E:K.106, E:G.137

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

CL.3: 4 residues within 4Å: Chain A: H.58, P.66, G.67 Ligands: EMO.4 Ligand excluded by PLIP CL.7: 3 residues within 4Å: Chain B: H.58, P.66, G.67 Ligand excluded by PLIP CL.8: 3 residues within 4Å: Chain C: H.58, G.67 Chain D: F.101 Ligand excluded by PLIP CL.11: 3 residues within 4Å: Chain D: H.58, P.66, G.67 Ligand excluded by PLIP CL.14: 3 residues within 4Å: Chain E: H.58, G.67 Chain F: F.101 Ligand excluded by PLIP CL.15: 3 residues within 4Å: Chain E: F.101 Chain F: H.58, G.67 Ligand excluded by PLIP

2 x EMO: 3-METHYL-1,6,8-TRIHYDROXYANTHRAQUINONE(Non-covalent)

EMO.4: 9 residues within 4Å: Chain A: F.59, F.109, R.110, I.111, P.112 Chain B: I.98, Y.100, E.159 Ligands: CL.3 9 PLIP interactions: 4 interactions with chain A, 5 interactions with chain B Hydrophobic interactions: A:F.59, B:I.98, B:Y.100 Hydrogen bonds: A:H.58 Water bridges: A:R.110, A:I.111, B:R.158 pi-Stacking: B:Y.100, B:Y.100 EMO.9: 16 residues within 4Å: Chain C: I.20, L.21, P.22, H.23, E.72, A.75, Q.76, G.79, F.80, F.83, K.97, I.98, V.99, F.101, R.158 Chain D: F.59 12 PLIP interactions: 12 interactions with chain C Hydrophobic interactions: C:I.20, C:L.21, C:F.83, C:V.99, C:V.99, C:F.101, C:F.101 Hydrogen bonds: C:E.72, C:K.97, C:V.99, C:R.158 pi-Stacking: C:H.23

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Chen, J. et al., Emodin targets the beta-hydroxyacyl-acyl carrier protein dehydratase from Helicobacter pylori: enzymatic inhibition assay with crystal structural and thermodynamic characterization. BMC MICROBIOL. (2009)

Release Date

2009-07-21

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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