SMTL ID : 3pn3.3 (2 other biounits)

Crystal structure of Arabidopsis thaliana petide deformylase 1B (AtPDF1B) in complex with inhibitor 21

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.30 Å

Oligo State

homo-dimer

Ligands

2 x PN3: tert-butyl {(2S)-1-[formyl(hydroxy)amino]-3-phenylpropan-2-yl}carbamate(Non-covalent)

PN3.1: 7 residues within 4Å: Chain A: Y.80, L.84, V.102, R.103, P.104, R.146 Ligands: ZN.9 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:Y.80, A:L.84, A:P.104 Hydrogen bonds: A:R.146, A:R.146 Water bridges: A:D.136 PN3.10: 7 residues within 4Å: Chain B: Y.80, L.84, V.102, R.103, P.104, R.146 Ligands: ZN.17 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:Y.80, B:L.84, B:P.104 Hydrogen bonds: B:R.146, B:R.146 Water bridges: B:E.139, B:E.139, B:E.139

15 x ZN: ZINC ION(Non-covalent)(Non-functional Binders)

ZN.2: 5 residues within 4Å: Chain A: Q.48, C.91, H.133, H.137 Ligands: ZN.3 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:C.91, A:H.133, A:H.137, H2O.7 ZN.3: 4 residues within 4Å: Chain A: Q.48, E.134, H.137 Ligands: ZN.2 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.134, A:E.134, H2O.1, H2O.7 ZN.4: 4 residues within 4Å: Chain A: D.40, G.62, E.63 Chain B: K.38 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.40, A:E.63, H2O.1, H2O.7, H2O.7 ZN.5: 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.7 ZN.6: 5 residues within 4Å: Chain A: D.30, D.34 Chain B: Y.37, E.69 Ligands: ZN.7 5 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: A:D.30, A:D.30, A:D.34, B:E.69, H2O.7 ZN.7: 6 residues within 4Å: Chain A: D.30, D.34 Chain B: D.30, D.34 Ligands: ZN.6, ZN.15 4 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: B:D.34, A:D.34, H2O.7, H2O.18 ZN.8: 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.9: 1 residues within 4Å: Ligands: PN3.1 No protein-ligand interaction detected (PLIP) ZN.11: 5 residues within 4Å: Chain B: Q.48, C.91, H.133, H.137 Ligands: ZN.12 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:C.91, B:H.133, B:H.137, H2O.18 ZN.12: 3 residues within 4Å: Chain B: Q.48, E.134 Ligands: ZN.11 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.134, B:E.134, H2O.13, H2O.18 ZN.13: 4 residues within 4Å: Chain A: K.38 Chain B: D.40, G.62, E.63 5 PLIP interactions: 2 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.40, B:E.63, H2O.13, H2O.17, H2O.18 ZN.14: 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.18 ZN.15: 5 residues within 4Å: Chain A: Y.37, E.69 Chain B: D.30, D.34 Ligands: ZN.7 5 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: B:D.30, B:D.30, B:D.34, A:E.69, H2O.18 ZN.16: 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.17: 1 residues within 4Å: Ligands: PN3.10 No protein-ligand interaction detected (PLIP)

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
B

Peptide deformylase 1B, chloroplastic

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