SMTL ID : 1q91.1

Crystal structure of human mitochondrial deoxyribonucleotidase in complex with the inhibitor DPB-T

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

monomer

Ligands

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

PO4.1: 9 residues within 4Å: Chain A: D.10, M.11, D.12, T.99, S.100, K.112, K.134 Ligands: MG.2, DPB.3 12 PLIP interactions: 12 interactions with chain A Hydrogen bonds: A:D.10, A:D.10, A:M.11, A:D.12, A:T.99, A:S.100 Water bridges: A:S.100, A:K.112, A:K.134, A:K.134 Salt bridges: A:K.112, A:K.134

1 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 5 residues within 4Å: Chain A: D.10, D.12, D.144, D.145 Ligands: PO4.1 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.10, A:D.12, A:D.145, H2O.211, H2O.314

1 x DPB: (S)-1-[2'-DEOXY-3',5'-O-(1-PHOSPHONO)BENZYLIDENE-B-D-THREO-PENTOFURANOSYL]THYMINE(Non-covalent)

DPB.3: 12 residues within 4Å: Chain A: D.12, F.18, F.44, W.45, V.46, W.65, S.100, P.101, I.102, K.103, R.132 Ligands: PO4.1 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:D.12, A:F.44, A:W.45, A:W.65, A:I.102 Hydrogen bonds: A:F.44, A:V.46, A:K.103, A:R.132, A:R.132 Water bridges: A:S.47, A:M.104 pi-Stacking: A:F.18, A:W.45 pi-Cation interactions: A:R.132

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Rinaldo-Matthis, A. et al., Crystal structures of the mitochondrial deoxyribonucleotidase in complex with two specific inhibitors. Mol.Pharmacol. (2004)

Release Date

2004-04-20

Peptides

5(3)-deoxyribonucleotidase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

5(3)-deoxyribonucleotidase

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