SMTL ID : 3qu1.1

Peptide deformylase from Vibrio cholerae

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-dimer

Ligands

7 x ZN: ZINC ION(Non-covalent)

ZN.1: 6 residues within 4Å: Chain A: Q.54, C.94, H.136, H.140 Chain B: R.171 Ligands: ZN.3 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:C.94, A:H.136, A:H.140, H2O.2 ZN.2: 6 residues within 4Å: Chain A: D.99, H.165, R.171 Chain B: D.99, Y.101 Ligands: ZN.4 4 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: A:D.99, A:H.165, B:Y.101, H2O.7 ZN.3: 6 residues within 4Å: Chain A: G.49, L.50, H.136, E.137 Chain B: R.171 Ligands: ZN.1 5 PLIP interactions: 1 interactions with chain B, 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: B:R.171, A:G.49, A:E.137, A:E.137, H2O.2 ZN.4: 4 residues within 4Å: Chain A: D.99 Chain B: D.99 Ligands: ZN.2, ZN.6 6 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B, 4 Ligand-Water interactions Metal complexes: A:D.99, B:D.99, H2O.2, H2O.4, H2O.7, H2O.7 ZN.6: 5 residues within 4Å: Chain A: Y.101 Chain B: D.99, H.165, R.171 Ligands: ZN.4 5 PLIP interactions: 1 interactions with chain A, 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: A:Y.101, B:D.99, B:D.99, B:H.165, H2O.2 ZN.7: 5 residues within 4Å: Chain B: Q.54, C.94, H.136, H.140 Ligands: ZN.8 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:C.94, B:H.136, B:H.140, H2O.8 ZN.8: 6 residues within 4Å: Chain A: R.171 Chain B: G.49, L.50, H.136, E.137 Ligands: ZN.7 5 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: B:G.49, B:E.137, A:R.171, H2O.8, H2O.11

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

CL.5: 3 residues within 4Å: Chain A: P.13, D.14, R.18 Ligand excluded by PLIP CL.9: 4 residues within 4Å: Chain B: A.12, P.13, D.14, R.18 Ligand excluded by PLIP

1 x SO4: SULFATE ION(Non-functional Binders)

SO4.10: 3 residues within 4Å: Chain B: T.11, P.13, D.14 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:T.11, B:P.13, B:D.14 Water bridges: B:T.11

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Osipiuk, J. et al., Peptide deformylase from Vibrio cholerae. To be Published

Release Date

2011-03-09

Peptides

Peptide deformylase 2: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Peptide deformylase 2