SMTL ID : 5buw.1

Crystal Structure of beta-hydroxyacyl-acyl carrier protein dehydratase (FabZ) from Yersinia Pestis

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-hexamer

Ligands

9 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.1: 5 residues within 4Å: Chain A: H.34, E.83, Y.106 Chain B: H.69 Ligands: SCN.5 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:H.69 EDO.2: 6 residues within 4Å: Chain A: P.37, P.64, F.65 Chain B: P.37, P.64, F.65 No protein-ligand interaction detected (PLIP) EDO.4: 5 residues within 4Å: Chain A: H.69 Chain B: H.34, E.83, Y.106 Ligands: SCN.3 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:H.69 Water bridges: A:G.78 EDO.8: 5 residues within 4Å: Chain C: H.34, E.83, Y.106 Chain D: H.69 Ligands: SCN.12 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:H.69 EDO.9: 6 residues within 4Å: Chain C: P.37, P.64, F.65 Chain D: P.37, P.64, F.65 No protein-ligand interaction detected (PLIP) EDO.11: 5 residues within 4Å: Chain C: H.69 Chain D: H.34, E.83, Y.106 Ligands: SCN.10 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:H.69 Water bridges: C:G.78 EDO.15: 5 residues within 4Å: Chain E: H.34, E.83, Y.106 Chain F: H.69 Ligands: SCN.19 1 PLIP interactions: 1 interactions with chain F Hydrogen bonds: F:H.69 EDO.16: 6 residues within 4Å: Chain E: P.37, P.64, F.65 Chain F: P.37, P.64, F.65 No protein-ligand interaction detected (PLIP) EDO.18: 5 residues within 4Å: Chain E: H.69 Chain F: H.34, E.83, Y.106 Ligands: SCN.17 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:H.69 Water bridges: E:G.78

12 x SCN: THIOCYANATE ION(Non-functional Binders)

SCN.3: 7 residues within 4Å: Chain A: H.69, P.77, G.78 Chain B: Y.106, Y.107, F.108 Ligands: EDO.4 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.78 SCN.5: 7 residues within 4Å: Chain A: Y.106, Y.107, F.108 Chain B: H.69, P.77, G.78 Ligands: EDO.1 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:G.78 SCN.6: 5 residues within 4Å: Chain B: G.50, L.92, A.93, S.96, F.142 No protein-ligand interaction detected (PLIP) SCN.7: 1 residues within 4Å: Chain B: R.97 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.97, B:R.97 SCN.10: 7 residues within 4Å: Chain C: H.69, P.77, G.78 Chain D: Y.106, Y.107, F.108 Ligands: EDO.11 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:G.78 SCN.12: 7 residues within 4Å: Chain C: Y.106, Y.107, F.108 Chain D: H.69, P.77, G.78 Ligands: EDO.8 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:G.78 SCN.13: 5 residues within 4Å: Chain D: G.50, L.92, A.93, S.96, F.142 No protein-ligand interaction detected (PLIP) SCN.14: 1 residues within 4Å: Chain D: R.97 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:R.97, D:R.97 SCN.17: 7 residues within 4Å: Chain E: H.69, P.77, G.78 Chain F: Y.106, Y.107, F.108 Ligands: EDO.18 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:G.78 SCN.19: 7 residues within 4Å: Chain E: Y.106, Y.107, F.108 Chain F: H.69, P.77, G.78 Ligands: EDO.15 1 PLIP interactions: 1 interactions with chain F Hydrogen bonds: F:G.78 SCN.20: 5 residues within 4Å: Chain F: G.50, L.92, A.93, S.96, F.142 No protein-ligand interaction detected (PLIP) SCN.21: 1 residues within 4Å: Chain F: R.97 2 PLIP interactions: 2 interactions with chain F Hydrogen bonds: F:R.97, F:R.97

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Mcgillick, B. et al., Crystal Structure of beta-hydroxyacyl-acyl carrier protein dehydratase (FabZ) from Yersinia Pestis. To be published

Release Date

2016-06-15

Peptides

3-hydroxyacyl-[acyl-carrier-protein] dehydratase FabZ: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

E
A

F
B

3-hydroxyacyl-[acyl-carrier-protein] dehydratase FabZ