SMTL ID : 3cmd.1 (1 other biounit)

Crystal structure of peptide deformylase from VRE-E.faecium

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.70 Å

Oligo State

monomer

Ligands

1 x FE: FE (III) ION(Non-covalent)

FE.1: 5 residues within 4Å: Chain A: Q.74, C.123, H.166, H.170 Ligands: MLI.4 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:C.123, A:H.166, A:H.170

2 x NA: SODIUM ION(Non-functional Binders)

NA.2: 3 residues within 4Å: Chain A: E.121, G.122, H.166 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.122 NA.3: 2 residues within 4Å: Chain A: M.9, E.45 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.45

3 x MLI: MALONATE ION(Non-functional Binders)

MLI.4: 11 residues within 4Å: Chain A: G.67, V.68, G.69, Q.74, G.122, C.123, L.124, H.166, E.167, H.170 Ligands: FE.1 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:V.68, A:G.69, A:Q.74, A:G.122, A:L.124 Salt bridges: A:H.166, A:H.170 MLI.5: 4 residues within 4Å: Chain A: V.31, S.32, D.39, K.79 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.32 Water bridges: A:D.39, A:K.79 Salt bridges: A:K.79 MLI.6: 3 residues within 4Å: Chain A: E.19, R.25, Y.177 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.19 Salt bridges: A:R.25, A:R.25

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nam, K.H. et al., Insight into the antibacterial drug design and architectural mechanism of peptide recognition from the E. faecium peptide deformylase structure. Proteins (2009)

Release Date

2009-01-13

Peptides

Peptide deformylase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Peptide deformylase

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