SMTL ID : 2glp.1

Crystal structure of (3R)-Hydroxyacyl-Acyl Carrier Protein Dehydratase(FabZ) from Helicobacter pylori complexed with compound 1

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.42 Å

Oligo State

homo-hexamer

Ligands

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

CL.1: 2 residues within 4Å: Chain A: H.70, G.79 Ligand excluded by PLIP CL.8: 3 residues within 4Å: Chain B: H.70, P.78, G.79 Ligand excluded by PLIP CL.11: 3 residues within 4Å: Chain C: H.70, G.79 Chain D: F.113 Ligand excluded by PLIP CL.14: 3 residues within 4Å: Chain D: H.70, P.78, G.79 Ligand excluded by PLIP CL.15: 3 residues within 4Å: Chain E: H.70, G.79 Chain F: F.113 Ligand excluded by PLIP CL.16: 3 residues within 4Å: Chain E: F.113 Chain F: H.70, G.79 Ligand excluded by PLIP

10 x BEN: BENZAMIDINE(Non-functional Binders)

BEN.2: 5 residues within 4Å: Chain A: Q.21, Q.23, F.24, H.28, F.101 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:Q.21, A:Q.21, A:F.24, A:F.24 Hydrogen bonds: A:Q.23 pi-Stacking: A:H.28, A:F.101 BEN.3: 11 residues within 4Å: Chain A: I.32, L.33, P.34, H.35, G.91, F.95, A.106, K.109, I.110, V.111, R.170 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:I.32, A:L.33, A:F.95, A:F.95, A:V.111 Hydrogen bonds: A:V.111, A:V.111 Water bridges: A:Q.88 BEN.4: 4 residues within 4Å: Chain A: Q.52, E.136, V.137, L.138 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:E.136, A:L.138 Hydrogen bonds: A:Q.52, A:Q.52, A:E.136 BEN.5: 3 residues within 4Å: Chain A: G.149, T.150, E.160 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:T.150 Water bridges: A:G.148, A:G.149, A:G.149 BEN.6: 4 residues within 4Å: Chain A: M.143, I.144, M.166, I.167 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:I.144 BEN.9: 9 residues within 4Å: Chain B: I.32, L.33, P.34, H.35, F.95, A.106, K.109, I.110, V.111 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:I.32, B:L.33, B:F.95, B:F.95, B:I.110, B:V.111 Hydrogen bonds: B:V.111 BEN.10: 2 residues within 4Å: Chain B: W.99, G.100 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:W.99 BEN.12: 6 residues within 4Å: Chain C: A.50, T.96, S.97, L.98, W.99, G.100 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:T.96 BEN.17: 9 residues within 4Å: Chain E: P.38, M.39, D.65, V.66, L.81 Chain F: P.38, M.39, V.66, L.81 9 PLIP interactions: 5 interactions with chain E, 1 interactions with chain C, 3 interactions with chain F Hydrophobic interactions: E:L.81, F:P.38, F:V.66, F:L.81 Hydrogen bonds: E:P.38, E:D.65, E:V.66 Water bridges: E:D.65, C:N.63 BEN.18: 6 residues within 4Å: Chain F: K.53, H.134, L.135, E.136, G.148, G.149 4 PLIP interactions: 4 interactions with chain F Hydrophobic interactions: F:K.53, F:H.134, F:E.136 Hydrogen bonds: F:E.136

2 x BDE: N'-[(1E)-(3,5-DIBROMO-2,4-DIHYDROXYPHENYL)METHYLENE]NICOTINOHYDRAZIDE(Non-covalent)

BDE.7: 10 residues within 4Å: Chain A: F.71, K.74, I.76, I.123, P.124 Chain B: P.34, I.110, Y.112, R.170, E.171 8 PLIP interactions: 5 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:I.110, B:I.110, B:Y.112, B:Y.112, B:Y.112, A:F.71, A:I.76 Water bridges: A:I.123 BDE.13: 13 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 Chain D: F.71, K.74, I.76 6 PLIP interactions: 5 interactions with chain C, 1 interactions with chain D Hydrophobic interactions: C:K.109, C:I.110, C:V.111 Hydrogen bonds: C:V.111, C:R.170 pi-Stacking: D:F.71

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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