SMTL ID : 2glm.1

Crystal structure of (3R)-Hydroxyacyl-Acyl Carrier Protein Dehydratase(FabZ) from Helicobacter pylori complexed with Compound 2

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.60 Å

Oligo State

homo-hexamer

Ligands

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

CL.1: 4 residues within 4Å: Chain A: H.70, P.78, G.79 Ligands: SCB.4 Ligand excluded by PLIP CL.5: 3 residues within 4Å: Chain B: H.70, P.78, G.79 Ligand excluded by PLIP CL.7: 3 residues within 4Å: Chain C: H.70, G.79 Chain D: F.113 Ligand excluded by PLIP CL.10: 3 residues within 4Å: Chain D: H.70, P.78, G.79 Ligand excluded by PLIP CL.13: 2 residues within 4Å: Chain E: G.79 Chain F: F.113 Ligand excluded by PLIP CL.14: 3 residues within 4Å: Chain E: F.113 Chain F: H.70, G.79 Ligand excluded by PLIP

7 x BEN: BENZAMIDINE(Non-functional Binders)

BEN.2: 3 residues within 4Å: Chain A: Q.52, E.136, V.137 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:E.136, A:E.136, A:E.136 Hydrogen bonds: A:Q.52, A:E.136 BEN.3: 3 residues within 4Å: Chain A: K.118, E.160, E.162 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:K.118 Hydrogen bonds: A:E.160 pi-Cation interactions: A:K.118 BEN.6: 9 residues within 4Å: Chain B: I.32, L.33, P.34, H.35, F.95, A.106, K.109, V.111, R.170 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:I.32, B:L.33, B:F.95, B:F.95, B:A.106, B:K.109, B:V.111 Hydrogen bonds: B:V.111, B:V.111 BEN.8: 10 residues within 4Å: Chain C: I.32, L.33, P.34, H.35, F.95, A.106, K.109, I.110, V.111, R.170 6 PLIP interactions: 6 interactions with chain C Hydrophobic interactions: C:L.33, C:F.95, C:V.111, C:V.111 Hydrogen bonds: C:H.35, C:V.111 BEN.9: 6 residues within 4Å: Chain C: A.50, T.96, S.97, L.98, W.99, G.100 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:S.97 Water bridges: C:Q.21, C:Q.21 BEN.11: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) BEN.12: 4 residues within 4Å: Chain E: L.98, W.99, G.142, M.143 4 PLIP interactions: 4 interactions with chain E Hydrophobic interactions: E:L.98, E:L.98, E:W.99 Water bridges: E:G.142

1 x SCB: 2-CHLORO-5-(5-{(E)-[(2Z)-3-(2-METHOXYETHYL)-4-OXO-2-(PHENYLIMINO)-1,3-THIAZOLIDIN-5-YLIDENE]METHYL}-2-FURYL)BENZOIC ACID(Non-covalent)

SCB.4: 16 residues within 4Å: Chain A: F.71, P.72, N.73, K.74, I.76, F.121, R.122, I.123, P.124 Chain B: P.34, I.110, V.111, Y.112, F.113, R.170 Ligands: CL.1 11 PLIP interactions: 6 interactions with chain B, 5 interactions with chain A Hydrophobic interactions: B:I.110, B:R.170, A:F.71, A:F.71, A:F.71, A:K.74, A:I.76 Hydrogen bonds: B:F.113 Salt bridges: B:R.170 pi-Stacking: B:Y.112 pi-Cation interactions: B:R.170

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhang, L. et al., Structural basis for catalytic and inhibitory mechanisms of beta-hydroxyacyl-acyl carrier protein dehydratase (FabZ). J.Biol.Chem. (2008)

Release Date

2007-03-13

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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