SMTL ID : 4je7.1

Crystal structure of a human-like mitochondrial peptide deformylase in complex with actinonin

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-dimer

Ligands

2 x BB2: ACTINONIN(Non-covalent)

BB2.1: 18 residues within 4Å: Chain A: P.46, C.47, V.48, G.49, Q.54, R.84, E.109, G.110, C.111, E.112, R.118, W.146, R.149, I.150, H.153, E.154, H.157 Ligands: ZN.2 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:V.48, A:V.48, A:W.146, A:R.149, A:I.150, A:H.153 Hydrogen bonds: A:V.48, A:G.49, A:Q.54, A:G.110, A:E.112 Water bridges: A:G.110 BB2.3: 18 residues within 4Å: Chain B: P.46, C.47, V.48, G.49, Q.54, R.84, E.109, G.110, C.111, E.112, R.118, W.146, R.149, I.150, H.153, E.154, H.157 Ligands: ZN.4 15 PLIP interactions: 15 interactions with chain B Hydrophobic interactions: B:V.48, B:V.48, B:E.109, B:E.112, B:W.146, B:R.149, B:I.150, B:H.153 Hydrogen bonds: B:V.48, B:Q.54, B:G.110, B:E.112, B:E.154 Water bridges: B:R.84, B:G.110

2 x ZN: ZINC ION(Non-covalent)

ZN.2: 5 residues within 4Å: Chain A: Q.54, C.111, H.153, H.157 Ligands: BB2.1 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:C.111, A:H.153, A:H.157 ZN.4: 5 residues within 4Å: Chain B: Q.54, C.111, H.153, H.157 Ligands: BB2.3 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:C.111, B:H.153, B:H.157

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Fieulaine, S. et al., Understanding the highly efficient catalysis of prokaryotic peptide deformylases by shedding light on the determinants specifying the low activity of the human counterpart. Acta Crystallogr.,Sect.D (2014)

Release Date

2014-02-26

Peptides

Peptide deformylase 1A, chloroplastic/mitochondrial: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Peptide deformylase 1A, chloroplastic/mitochondrial

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