SMTL ID : 3m6r.1 (3 other biounits)

Crystal structure of Arabidopsis thaliana peptide deformylase 1B (AtPDF1B) G41M mutant in complex with actinonin

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

monomer

Ligands

1 x BB2: ACTINONIN(Non-covalent)

BB2.1: 18 residues within 4Å: Chain A: D.40, M.41, I.42, G.43, Q.48, F.87, D.88, E.89, G.90, C.91, L.92, Y.98, R.129, I.130, H.133, E.134, H.137 Ligands: ZN.2 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:M.41, A:E.89, A:Y.98, A:R.129, A:H.133 Hydrogen bonds: A:I.42, A:G.43, A:Q.48, A:G.90, A:G.90, A:L.92, A:E.134

5 x ZN: ZINC ION(Non-covalent)

ZN.2: 5 residues within 4Å: Chain A: Q.48, C.91, H.133, H.137 Ligands: BB2.1 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:C.91, A:H.133, A:H.137 ZN.3: 3 residues within 4Å: Chain A: D.30, D.34 Ligands: ZN.4 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.30, A:D.30, A:D.34 ZN.4: 3 residues within 4Å: Chain A: D.30, D.34 Ligands: ZN.3 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:D.34 ZN.5: 1 residues within 4Å: Chain A: D.88 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:D.88 ZN.6: 2 residues within 4Å: Chain A: D.40, E.63 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.40, H2O.3

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Fieulaine, S. et al., Trapping conformational states along ligand-binding dynamics of peptide deformylase: the impact of induced fit on enzyme catalysis. Plos Biol. (2011)

Release Date

2011-03-30

Peptides

Peptide deformylase 1B: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Peptide deformylase 1B

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