SMTL ID : 1ix1.1

Crystal Structure of P.aeruginosa Peptide deformylase Complexed with Antibiotic Actinonin

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.85 Å

Oligo State

homo-dimer

Ligands

2 x ZN: ZINC ION(Non-covalent)

ZN.1: 5 residues within 4Å: Chain A: Q.51, C.92, H.134, H.138 Ligands: BB2.2 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:C.92, A:H.134, A:H.138 ZN.4: 5 residues within 4Å: Chain B: Q.51, C.92, H.134, H.138 Ligands: BB2.5 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:C.92, B:H.134, B:H.138

2 x BB2: ACTINONIN(Non-covalent)

BB2.2: 17 residues within 4Å: Chain A: G.44, I.45, G.46, Q.51, Y.88, Q.89, E.90, G.91, C.92, L.93, Y.99, V.130, C.131, H.134, E.135, H.138 Ligands: ZN.1 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:I.45, A:I.45, A:Y.88, A:E.90, A:L.93, A:L.93, A:Y.99, A:V.130 Hydrogen bonds: A:I.45, A:G.46, A:Q.51, A:G.91, A:G.91, A:L.93, A:E.135 BB2.5: 17 residues within 4Å: Chain B: G.44, I.45, G.46, Q.51, Y.88, Q.89, E.90, G.91, C.92, L.93, Y.99, V.130, C.131, H.134, E.135, H.138 Ligands: ZN.4 15 PLIP interactions: 15 interactions with chain B Hydrophobic interactions: B:I.45, B:I.45, B:Y.88, B:E.90, B:L.93, B:L.93, B:Y.99, B:V.130 Hydrogen bonds: B:I.45, B:G.46, B:Q.51, B:G.91, B:G.91, B:L.93, B:E.135

2 x MHA: (CARBAMOYLMETHYL-CARBOXYMETHYL-AMINO)-ACETIC ACID(Non-covalent)

MHA.3: 9 residues within 4Å: Chain A: R.71, V.72, F.73, D.114, R.115, F.120, E.122 Chain B: R.109, E.121 10 PLIP interactions: 5 interactions with chain B, 5 interactions with chain A Hydrogen bonds: B:E.121, A:V.72, A:R.115 Water bridges: B:R.109, B:R.109, B:K.111 Salt bridges: B:E.121, A:R.71, A:R.115, A:E.122 MHA.6: 10 residues within 4Å: Chain A: K.107, R.109, V.123 Chain B: R.71, V.72, F.73, D.114, R.115, F.120, E.122 9 PLIP interactions: 5 interactions with chain A, 4 interactions with chain B Hydrogen bonds: A:R.109, B:V.72, B:R.115 Water bridges: A:K.107, A:K.107, A:K.107 Salt bridges: A:K.107, B:R.71, B:R.115

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yoon, H.-J. et al., Crystal structure of peptide deformylase from Staphylococcus aureus in complex with actinonin, a naturally occurring antibacterial agent. Proteins (2004)

Release Date

2003-09-09

Peptides

peptide deformylase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

peptide deformylase