SMTL ID : 1z4i.1

Structure of the D41N variant of the human mitochondrial deoxyribonucleotidase in complex with deoxyribouridine 5'-monophosphate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.98 Å

Oligo State

homo-dimer

Ligands

2 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 5 residues within 4Å: Chain A: N.10, D.12, D.145 Ligands: UMP.2, GOL.3 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.12, A:D.145, H2O.4 MG.4: 5 residues within 4Å: Chain B: N.10, D.12, D.145 Ligands: UMP.5, GOL.6 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.12, B:D.145, H2O.12

2 x UMP: 2'-DEOXYURIDINE 5'-MONOPHOSPHATE(Non-covalent)

UMP.2: 17 residues within 4Å: Chain A: N.10, M.11, D.12, F.18, F.44, W.45, V.46, S.47, W.65, F.71, T.99, S.100, P.101, I.102, K.112 Ligands: MG.1, GOL.3 17 PLIP interactions: 17 interactions with chain A Hydrophobic interactions: A:F.18, A:I.102 Hydrogen bonds: A:N.10, A:M.11, A:D.12, A:V.46, A:S.47, A:T.99, A:T.99, A:S.100 Water bridges: A:N.10, A:S.47, A:S.100, A:S.100, A:K.112, A:K.134 Salt bridges: A:K.112 UMP.5: 17 residues within 4Å: Chain B: N.10, M.11, D.12, F.18, F.44, W.45, V.46, S.47, W.65, F.71, T.99, S.100, P.101, I.102, K.112 Ligands: MG.4, GOL.6 17 PLIP interactions: 17 interactions with chain B Hydrophobic interactions: B:F.18, B:I.102 Hydrogen bonds: B:N.10, B:M.11, B:D.12, B:D.12, B:V.46, B:S.47, B:T.99, B:S.100 Water bridges: B:N.10, B:S.47, B:S.100, B:S.100, B:K.112, B:K.134 Salt bridges: B:K.112

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 10 residues within 4Å: Chain A: D.12, G.13, F.18, E.19, R.41, F.44, V.46, D.145 Ligands: MG.1, UMP.2 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.12, A:E.19, A:R.41 Water bridges: A:N.10 GOL.6: 10 residues within 4Å: Chain B: D.12, G.13, F.18, E.19, R.41, F.44, V.46, D.145 Ligands: MG.4, UMP.5 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:D.12, B:E.19, B:E.19, B:R.41 Water bridges: B:D.145

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wallden, K. et al., Structural basis for substrate specificity of the human mitochondrial deoxyribonucleotidase. STRUCTURE (2005)

Release Date

2005-07-26

Peptides

5'(3')-deoxyribonucleotidase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

5'(3')-deoxyribonucleotidase

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