SMTL ID : 3g5p.1 (2 other biounits)

Structure and activity of human mitochondrial peptide deformylase, a novel cancer target

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

homo-tetramer

Ligands

4 x CO: COBALT (II) ION(Non-covalent)

CO.1: 5 residues within 4Å: Chain A: Q.55, C.112, H.154, H.158 Ligands: PO4.3 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:H.154, A:H.158 CO.4: 5 residues within 4Å: Chain B: Q.55, C.112, H.154, H.158 Ligands: PO4.6 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:C.112, B:H.154, B:H.158 CO.7: 5 residues within 4Å: Chain C: Q.55, C.112, H.154, H.158 Ligands: PO4.9 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:H.154, C:H.158 CO.10: 5 residues within 4Å: Chain D: Q.55, C.112, H.154, H.158 Ligands: PO4.12 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:C.112, D:H.154, D:H.158

8 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.2: 6 residues within 4Å: Chain A: C.48, V.49, G.50, I.151, E.155 Ligands: PO4.3 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:V.49, A:G.50 Water bridges: A:G.111 PO4.3: 11 residues within 4Å: Chain A: C.48, G.50, L.51, Q.55, C.112, E.113, H.154, E.155, H.158 Ligands: CO.1, PO4.2 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:G.50, A:Q.55, A:E.113 Water bridges: A:G.111, A:H.154 Salt bridges: A:H.154 PO4.5: 6 residues within 4Å: Chain B: C.48, V.49, G.50, I.151, E.155 Ligands: PO4.6 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:V.49, B:G.50 Water bridges: B:G.111 PO4.6: 11 residues within 4Å: Chain B: C.48, G.50, L.51, Q.55, C.112, E.113, H.154, E.155, H.158 Ligands: CO.4, PO4.5 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:Q.55, B:E.113 Water bridges: B:G.111, B:H.154 Salt bridges: B:H.154 PO4.8: 6 residues within 4Å: Chain C: C.48, V.49, G.50, I.151, E.155 Ligands: PO4.9 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:V.49, C:G.50 Water bridges: C:G.111 PO4.9: 11 residues within 4Å: Chain C: C.48, G.50, L.51, Q.55, C.112, E.113, H.154, E.155, H.158 Ligands: CO.7, PO4.8 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:Q.55, C:E.113 Water bridges: C:G.111, C:H.154 Salt bridges: C:H.154 PO4.11: 6 residues within 4Å: Chain D: C.48, V.49, G.50, I.151, E.155 Ligands: PO4.12 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:V.49, D:G.50 Water bridges: D:G.111 PO4.12: 11 residues within 4Å: Chain D: C.48, G.50, L.51, Q.55, C.112, E.113, H.154, E.155, H.158 Ligands: CO.10, PO4.11 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:Q.55, D:G.111, D:E.113 Salt bridges: D:H.154

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Escobar-Alvarez, S. et al., Structure and activity of human mitochondrial peptide deformylase, a novel cancer target. J.Mol.Biol. (2009)

Release Date

2009-04-07

Peptides

Peptide deformylase, mitochondrial: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Peptide deformylase, mitochondrial

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