SMTL ID : 1vev.1 (1 other biounit)

Crystal structure of peptide deformylase from Leptospira Interrogans (LiPDF) at pH6.5

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.51 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.4 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:C.101, A:H.143, A:H.147 ZN.5: 5 residues within 4Å: Chain B: Q.53, C.101, H.143, H.147 Ligands: FMT.8 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:C.101, B:H.143, B:H.147

4 x MES: 2-(N-MORPHOLINO)-ETHANESULFONIC ACID(Non-covalent)

MES.2: 15 residues within 4Å: Chain A: G.46, V.47, G.48, R.70, Y.71, F.97, E.99, G.100, C.101, L.102, Y.136, I.139, V.140, H.143 Ligands: FMT.4 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:V.47, A:G.48, A:L.102 Water bridges: A:E.99, A:G.100 Salt bridges: A:R.70 MES.3: 3 residues within 4Å: Chain A: P.78, R.80, K.137 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.80, A:R.80, A:K.137 MES.6: 15 residues within 4Å: Chain B: G.46, V.47, G.48, R.70, Y.71, F.97, E.99, G.100, C.101, L.102, Y.136, I.139, V.140, H.143 Ligands: FMT.8 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:V.47, B:G.48, B:Y.71, B:L.102 Water bridges: B:G.100, B:G.100 Salt bridges: B:R.70 MES.7: 3 residues within 4Å: Chain B: P.78, R.80, K.137 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.80, B:R.80, B:K.137

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

FMT.4: 10 residues within 4Å: Chain A: G.48, L.49, Q.53, C.101, L.102, H.143, E.144, H.147 Ligands: ZN.1, MES.2 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.53, A:L.102, A:E.144 FMT.8: 10 residues within 4Å: Chain B: G.48, L.49, Q.53, C.101, L.102, H.143, E.144, H.147 Ligands: ZN.5, MES.6 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Q.53, B:L.102, B:E.144

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
A

B
A

Peptide deformylase

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