SMTL ID : 5i2b.1

Crystal structure of a peptide deformylase from Burkholderia ambifaria with actinonin

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

homo-dimer

Ligands

2 x ZN: ZINC ION(Non-covalent)

ZN.1: 5 residues within 4Å: Chain A: Q.59, C.107, H.149, H.153 Ligands: BB2.2 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:C.107, A:H.149, A:H.153 ZN.8: 5 residues within 4Å: Chain B: Q.59, C.107, H.149, H.153 Ligands: BB2.9 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:C.107, B:H.149, B:H.153

2 x BB2: ACTINONIN(Non-covalent)

BB2.2: 21 residues within 4Å: Chain A: N.51, G.52, A.53, G.54, L.55, Q.59, R.76, Y.77, W.104, E.105, G.106, C.107, L.108, R.114, F.142, R.145, V.146, H.149, E.150, H.153 Ligands: ZN.1 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:E.105, A:F.142 Hydrogen bonds: A:A.53, A:G.54, A:Q.59, A:G.106, A:G.106, A:L.108 BB2.9: 21 residues within 4Å: Chain B: N.51, G.52, A.53, G.54, L.55, Q.59, R.76, Y.77, W.104, E.105, G.106, C.107, L.108, R.114, F.142, R.145, V.146, H.149, E.150, H.153 Ligands: ZN.8 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:E.105, B:F.142 Hydrogen bonds: B:A.53, B:G.54, B:Q.59, B:G.106, B:G.106, B:L.108

10 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.3: 5 residues within 4Å: Chain A: Y.95, S.118, R.119, Y.120, R.162 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.119 Water bridges: A:S.118, A:Y.120, A:Y.120, A:R.162 EDO.4: 2 residues within 4Å: Chain A: D.32, F.131 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.32, A:F.131 EDO.5: 2 residues within 4Å: Chain A: P.78, D.79 1 PLIP interactions: 1 interactions with chain A Water bridges: A:P.78 EDO.6: 5 residues within 4Å: Chain A: E.102, G.103, W.104, V.116, R.168 1 PLIP interactions: 1 interactions with chain A Water bridges: A:W.104 EDO.7: 5 residues within 4Å: Chain A: V.40, F.44, E.85, V.87, Q.130 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.130, A:Q.130 EDO.10: 5 residues within 4Å: Chain B: Y.95, S.118, R.119, Y.120, R.162 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.119 Water bridges: B:S.118, B:R.162 EDO.11: 2 residues within 4Å: Chain B: D.32, F.131 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:F.131 EDO.12: 2 residues within 4Å: Chain B: P.78, D.79 1 PLIP interactions: 1 interactions with chain B Water bridges: B:P.78 EDO.13: 5 residues within 4Å: Chain B: E.102, G.103, W.104, V.116, R.168 1 PLIP interactions: 1 interactions with chain B Water bridges: B:W.104 EDO.14: 5 residues within 4Å: Chain B: V.40, F.44, E.85, V.87, Q.130 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Q.130, B:Q.130

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Conrady, D.G. et al., Crystal structure of a peptide deformylase from Burkholderia ambifaria with actinonin. to be published

Release Date

2016-03-09

Peptides

Peptide deformylase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Peptide deformylase

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