SMTL ID : 1z4q.1

Structure of the D41N variant of the human mitochondrial deoxyribonucleotidase in complex with 2',3'-dideoxy-2',3-didehydrothymidine 5'-monophosphate (d4T-MP)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.05 Å

Oligo State

homo-dimer

Ligands

4 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 3 residues within 4Å: Chain A: A.88, L.90, T.93 6 PLIP interactions: 3 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:A.88, A:L.90, A:T.93, H2O.4, H2O.5, H2O.6 MG.2: 4 residues within 4Å: Chain A: N.10, D.12, D.145 Ligands: D4M.3 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.12, A:D.145, H2O.2, H2O.4 MG.4: 3 residues within 4Å: Chain B: A.88, L.90, T.93 6 PLIP interactions: 3 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:A.88, B:L.90, B:T.93, H2O.11, H2O.11, H2O.12 MG.5: 4 residues within 4Å: Chain B: N.10, D.12, D.145 Ligands: D4M.6 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.12, B:D.145, H2O.8, H2O.10

2 x D4M: [(5R)-5-(5-METHYL-2,4-DIOXO-3,4-DIHYDROPYRIMIDIN-1(2H)-YL)-2,5-DIHYDROFURAN-2-YL]METHYL DIHYDROGEN PHOSPHATE(Non-covalent)

D4M.3: 14 residues within 4Å: Chain A: N.10, D.12, F.18, F.44, W.45, V.46, S.47, W.65, F.71, T.99, S.100, I.102, K.134 Ligands: MG.2 19 PLIP interactions: 19 interactions with chain A Hydrophobic interactions: A:F.18, A:F.18, A:V.46, A:F.71, A:I.102 Hydrogen bonds: A:N.10, A:D.12, A:V.46, A:S.47, A:T.99, A:S.100 Water bridges: A:M.11, A:S.47, A:S.47, A:K.112, A:K.134, A:K.134, A:D.144 Salt bridges: A:K.134 D4M.6: 14 residues within 4Å: Chain B: N.10, D.12, F.18, F.44, W.45, V.46, S.47, W.65, F.71, T.99, S.100, I.102, K.134 Ligands: MG.5 18 PLIP interactions: 18 interactions with chain B Hydrophobic interactions: B:F.18, B:F.18, B:V.46, B:F.71, B:I.102 Hydrogen bonds: B:N.10, B:D.12, B:V.46, B:S.47, B:S.100 Water bridges: B:M.11, B:S.47, B:S.47, B:K.112, B:K.134, B:K.134, B:D.144 Salt bridges: B:K.134

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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