SMTL ID : 1q92.1

Crystal structure of human mitochondrial deoxyribonucleotidase in complex with the inhibitor PMcP-U

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.40 Å

Oligo State

monomer

Ligands

1 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 4 residues within 4Å: Chain A: D.10, D.12, D.144, D.145 6 PLIP interactions: 3 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.10, A:D.12, A:D.145, H2O.7, H2O.10, H2O.134

1 x DRM: {[(1R,2S)-2-(2,4-DIOXO-3,4-DIHYDROPYRIMIDIN-1(2H)-YL)CYCLOPENTYL]OXY}METHYLPHOSPHONIC ACID(Non-covalent)

DRM.2: 12 residues within 4Å: Chain A: D.10, D.12, F.18, F.44, W.45, V.46, F.71, S.100, P.101, I.102, K.134, R.146 19 PLIP interactions: 19 interactions with chain A Hydrophobic interactions: A:F.18, A:F.71, A:I.102 Hydrogen bonds: A:V.46, A:S.100, A:S.100, A:K.134, A:K.134, A:R.146 Water bridges: A:D.12, A:R.41, A:F.44, A:S.47, A:K.112, A:K.134, A:R.146 pi-Stacking: A:F.18, A:W.45, A:W.65

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 7 residues within 4Å: Chain A: R.42, G.43, H.167, N.168, Q.169, H.170, L.171 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.43, A:H.170, A:H.170, A:L.171

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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