SMTL ID : 1zy1.1

X-ray structure of peptide deformylase from Arabidopsis thaliana (AtPDF1A) in complex with Met-Ala-Ser

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.00 Å

Oligo State

homo-dimer

Ligands

2 x MET- ALA- SER: tripeptide fragment(Non-covalent)

MET-ALA-SER.1: 15 residues within 4Å: Chain A: P.46, G.47, V.48, G.49, L.50, R.84, E.109, G.110, C.111, L.112, R.118, R.149, I.150, H.153, E.154 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:V.48, A:H.153 Hydrogen bonds: A:P.46, A:V.48, A:G.49, A:R.84, A:G.110, A:E.154 MET-ALA-SER.2: 13 residues within 4Å: Chain B: P.46, G.47, V.48, G.49, R.84, E.109, G.110, L.112, R.118, R.149, I.150, H.153, E.154 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:V.48, B:L.112 Hydrogen bonds: B:P.46, B:V.48, B:G.49, B:R.84, B:G.110, B:E.154 Water bridges: B:P.46

2 x ZN: ZINC ION(Non-covalent)

ZN.3: 5 residues within 4Å: Chain A: Q.54, C.111, L.112, H.153, H.157 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:C.111, A:H.153, A:H.157, H2O.1, H2O.3 ZN.4: 4 residues within 4Å: Chain B: Q.54, C.111, H.153, H.157 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:C.111, B:H.153, B:H.157, H2O.2

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Fieulaine, S. et al., The crystal structure of mitochondrial (Type 1A) peptide deformylase provides clear guidelines for the design of inhibitors specific for the bacterial forms. J.Biol.Chem. (2005)

Release Date

2005-09-27

Peptides

Peptide deformylase, mitochondrial: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Peptide deformylase, mitochondrial

Related Entries With Identical Sequence