SMTL ID : 3pn4.2 (1 other biounit)

Crystal structure of Arabidopsis thaliana petide deformylase 1B (AtPDF1B) in complex with actinonin (crystallized in PEG-550-MME)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-dimer

Ligands

2 x BB2: ACTINONIN(Non-covalent)

BB2.1: 18 residues within 4Å: Chain A: D.40, G.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 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:E.89, A:L.92, A:L.92, A:Y.98, A:R.129, A:I.130, 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 BB2.7: 18 residues within 4Å: Chain B: D.40, G.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.8 14 PLIP interactions: 14 interactions with chain B Hydrophobic interactions: B:E.89, B:L.92, B:L.92, B:Y.98, B:R.129, B:I.130, B:H.133 Hydrogen bonds: B:I.42, B:G.43, B:Q.48, B:G.90, B:G.90, B:L.92, B:E.134

10 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: 2 residues within 4Å: Chain A: D.40, E.63 6 PLIP interactions: 1 interactions with chain A, 5 Ligand-Water interactions Metal complexes: A:D.40, H2O.3, H2O.7, H2O.8, H2O.8, H2O.9 ZN.4: 2 residues within 4Å: Chain A: E.160, E.179 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.160, A:E.160, A:E.179, H2O.10 ZN.5: 2 residues within 4Å: Chain A: M.1 Chain B: E.66 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:M.1 ZN.6: 4 residues within 4Å: Chain A: D.30, D.34 Chain B: Y.37, E.69 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain B Metal complexes: A:D.30, A:D.30, A:D.34, B:E.69, B:E.69 ZN.8: 5 residues within 4Å: Chain B: Q.48, C.91, H.133, H.137 Ligands: BB2.7 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:C.91, B:H.133, B:H.137 ZN.9: 2 residues within 4Å: Chain B: D.40, E.63 6 PLIP interactions: 1 interactions with chain B, 5 Ligand-Water interactions Metal complexes: B:D.40, H2O.13, H2O.17, H2O.18, H2O.18, H2O.19 ZN.10: 2 residues within 4Å: Chain B: E.160, E.179 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.160, B:E.160, B:E.179, H2O.19 ZN.11: 2 residues within 4Å: Chain A: E.66 Chain B: M.1 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:M.1 ZN.12: 4 residues within 4Å: Chain A: Y.37, E.69 Chain B: D.30, D.34 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain A Metal complexes: B:D.30, B:D.30, B:D.34, A:E.69, A:E.69

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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