SMTL ID : 1z4l.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-dimer

Ligands

4 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 4 residues within 4Å: Chain A: N.10, D.12, D.145 Ligands: TMP.3 5 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions, 1 Ligand-Ligand interactions Metal complexes: A:D.12, A:D.145, H2O.2, H2O.7, TMP.3 MG.2: 4 residues within 4Å: Chain A: A.88, S.89, L.90, T.93 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:A.88, A:L.90, H2O.5, H2O.5, H2O.6 MG.4: 4 residues within 4Å: Chain B: N.10, D.12, D.145 Ligands: TMP.6 5 PLIP interactions: 2 interactions with chain B, 1 Ligand-Ligand interactions, 2 Ligand-Water interactions Metal complexes: B:D.12, B:D.145, TMP.6, H2O.9, H2O.14 MG.5: 4 residues within 4Å: Chain B: A.88, S.89, L.90, T.93 5 PLIP interactions: 2 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:A.88, B:L.90, H2O.12, H2O.12, H2O.13

2 x TMP: THYMIDINE-5'-PHOSPHATE(Non-covalent)

TMP.3: 15 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, P.101, I.102, K.134 Ligands: MG.1 19 PLIP interactions: 19 interactions with chain A Hydrophobic interactions: A:F.18, A:F.18, A:V.46, A:I.102 Hydrogen bonds: A:N.10, A:N.10, A:N.10, A:D.12, A:V.46, A:S.47, A:S.100, A:S.100 Water bridges: A:M.11, A:S.47, A:T.99, A:K.134, A:K.134, A:R.146 Salt bridges: A:K.134 TMP.6: 15 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, P.101, I.102, K.134 Ligands: MG.4 19 PLIP interactions: 19 interactions with chain B Hydrophobic interactions: B:F.18, B:F.18, B:V.46, B:I.102 Hydrogen bonds: B:N.10, B:N.10, B:N.10, B:D.12, B:V.46, B:S.47, B:S.100, B:S.100 Water bridges: B:M.11, B:D.12, B:S.47, B:K.134, B:K.134, B:R.146 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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