SMTL ID : 1vez.2 (1 other biounit)

Crystal Structure of Peptide Deformylase from Leptospira Interrogans(LiPDF) at pH8.0

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-dimer

Ligands

2 x ZN: ZINC ION(Non-covalent)

ZN.1: 5 residues within 4Å: Chain A: Q.53, C.101, H.143, H.147 Ligands: FMT.6 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:C.101, A:H.143, A:H.147 ZN.9: 5 residues within 4Å: Chain B: Q.53, C.101, H.143, H.147 Ligands: FMT.14 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:C.101, B:H.143, B:H.147

14 x FMT: FORMIC ACID(Non-functional Binders)

FMT.2: 3 residues within 4Å: Chain A: R.80, K.137, Y.141 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.137, A:Y.141 Water bridges: A:Y.141 FMT.3: 2 residues within 4Å: Chain A: W.98, L.169 No protein-ligand interaction detected (PLIP) FMT.4: 2 residues within 4Å: Chain A: W.98, Y.110 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:W.98 FMT.5: 3 residues within 4Å: Chain A: G.55, I.56, L.57 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:L.57 FMT.6: 9 residues within 4Å: Chain A: G.48, Q.53, C.101, L.102, H.143, E.144, H.147 Ligands: ZN.1, FMT.7 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.53, A:L.102, A:E.144 FMT.7: 9 residues within 4Å: Chain A: G.46, V.47, G.48, R.70, Y.71, G.100, C.101, L.102 Ligands: FMT.6 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:V.47, A:G.48, A:R.70, A:R.70, A:G.100, A:L.102 FMT.8: 2 residues within 4Å: Chain A: Q.59, V.86 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.59 FMT.10: 3 residues within 4Å: Chain B: R.80, K.137, Y.141 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:K.137, B:Y.141, B:Y.141 Water bridges: B:R.80 FMT.11: 2 residues within 4Å: Chain B: W.98, L.169 No protein-ligand interaction detected (PLIP) FMT.12: 2 residues within 4Å: Chain B: W.98, Y.110 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:W.98 FMT.13: 3 residues within 4Å: Chain B: G.55, I.56, L.57 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:L.57 FMT.14: 9 residues within 4Å: Chain B: G.48, Q.53, C.101, L.102, H.143, E.144, H.147 Ligands: ZN.9, FMT.15 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Q.53, B:L.102, B:E.144 FMT.15: 9 residues within 4Å: Chain B: G.46, V.47, G.48, R.70, Y.71, G.100, C.101, L.102 Ligands: FMT.14 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:V.47, B:G.48, B:R.70, B:R.70, B:Y.71, B:G.100, B:L.102 FMT.16: 2 residues within 4Å: Chain B: Q.59, V.86 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Q.59

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhou, Z. et al., Novel conformational states of peptide deformylase from pathogenic bacterium Leptospira interrogans: implications for population shift. J.Biol.Chem. (2005)

Release Date

2005-08-23

Peptides

Peptide deformylase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
B

Peptide deformylase

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