SMTL ID : 3pn5.2 (1 other biounit)

Crystal structure of Arabidopsis thaliana petide deformylase 1B (AtPDF1B) G41Q mutant

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-dimer

Ligands

12 x ZN: ZINC ION(Non-covalent)

ZN.1: 5 residues within 4Å: Chain A: Q.48, C.91, H.133, H.137 Ligands: ZN.2 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:C.91, A:H.133, A:H.137, H2O.13 ZN.2: 5 residues within 4Å: Chain A: Q.41, Q.48, H.133, E.134 Ligands: ZN.1 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.134, A:E.134, H2O.13 ZN.3: 3 residues within 4Å: Chain A: D.40, G.62, E.63 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.40, A:E.63, H2O.13 ZN.4: 2 residues within 4Å: Chain A: E.160, E.179 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:E.160, A:E.179 ZN.5: 4 residues within 4Å: Chain A: D.30, D.34 Chain B: Y.37, E.69 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Metal complexes: B:E.69, B:E.69, A:D.30, A:D.34 ZN.6: 3 residues within 4Å: Chain A: M.1, E.2 Chain B: E.66 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:M.1 ZN.7: 5 residues within 4Å: Chain B: Q.48, C.91, H.133, H.137 Ligands: ZN.8 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:C.91, B:H.133, B:H.137, H2O.26 ZN.8: 5 residues within 4Å: Chain B: Q.41, Q.48, H.133, E.134 Ligands: ZN.7 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.134, B:E.134, H2O.26 ZN.9: 3 residues within 4Å: Chain B: D.40, G.62, E.63 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.40, B:E.63, H2O.26 ZN.10: 2 residues within 4Å: Chain B: E.160, E.179 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:E.160, B:E.179 ZN.11: 4 residues within 4Å: Chain A: Y.37, E.69 Chain B: D.30, D.34 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Metal complexes: B:D.30, B:D.34, A:E.69, A:E.69 ZN.12: 3 residues within 4Å: Chain A: E.66 Chain B: M.1, E.2 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:M.1

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

2011-06-08

Peptides

Peptide deformylase 1B, chloroplastic: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Peptide deformylase 1B, chloroplastic

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