SMTL ID : 1lru.4 (3 other biounits)

Crystal Structure of E.coli Peptide Deformylase Complexed with Antibiotic Actinonin

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-dimer

Ligands

2 x ZN: ZINC ION(Non-covalent)

ZN.1: 5 residues within 4Å: Chain A: Q.50, C.90, H.132, H.136 Ligands: BB2.4 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:C.90, A:H.132, A:H.136 ZN.5: 5 residues within 4Å: Chain B: Q.50, C.90, H.132, H.136 Ligands: BB2.6 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:C.90, B:H.132, B:H.136

2 x SO4: SULFATE ION(Non-functional Binders)

SO4.2: 4 residues within 4Å: Chain A: I.53, H.54, Q.55 Chain B: R.29 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:D.52, A:H.54, A:Q.55 Salt bridges: B:R.29 SO4.3: 4 residues within 4Å: Chain A: R.29 Chain B: I.53, H.54, Q.55 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:D.52, B:H.54, B:Q.55 Water bridges: A:S.1 Salt bridges: A:R.29

2 x BB2: ACTINONIN(Non-covalent)

BB2.4: 20 residues within 4Å: Chain A: E.42, G.43, I.44, G.45, L.46, Q.50, I.86, E.87, E.88, G.89, C.90, L.91, R.97, L.125, I.128, C.129, H.132, E.133, H.136 Ligands: ZN.1 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:E.88, A:L.125, A:I.128, A:H.132 Hydrogen bonds: A:I.44, A:Q.50, A:E.87, A:G.89, A:G.89, A:L.91, A:E.133 BB2.6: 16 residues within 4Å: Chain B: G.43, I.44, G.45, Q.50, E.87, E.88, G.89, C.90, L.91, R.97, I.128, C.129, H.132, E.133, H.136 Ligands: ZN.5 12 PLIP interactions: 12 interactions with chain B Hydrophobic interactions: B:I.44, B:E.88, B:L.91, B:I.128 Hydrogen bonds: B:I.44, B:G.45, B:Q.50, B:G.89, B:G.89, B:L.91, B:R.97, B:H.136

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Guilloteau, J.P. et al., The crystal structures of four peptide deformylases bound to the antibiotic actinonin reveal two distinct types: a platform for the structure-based design of antibacterial agents. J.Mol.Biol. (2002)

Release Date

2002-07-24

Peptides

PEPTIDE DEFORMYLASE: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
C

PEPTIDE DEFORMYLASE

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