SMTL ID : 1z4k.1

Structure of the D41N variant of the human mitochondrial deoxyribonucleotidase in complex with thymidine 3'-monophosphate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.75 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.144, D.145 Ligands: T3P.2 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.12, A:D.145, H2O.4, H2O.5 MG.3: 5 residues within 4Å: Chain B: N.10, D.12, D.144, D.145 Ligands: T3P.4 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.12, B:D.145, H2O.11, H2O.12

2 x T3P: THYMIDINE-3'-PHOSPHATE(Non-covalent)

T3P.2: 14 residues within 4Å: Chain A: N.10, M.11, D.12, F.18, F.44, W.45, V.46, W.65, T.99, S.100, P.101, I.102, K.112 Ligands: MG.1 20 PLIP interactions: 20 interactions with chain A Hydrophobic interactions: A:F.44, A:W.45, A:W.45, A:W.65 Hydrogen bonds: A:N.10, A:N.10, A:M.11, A:D.12, A:F.44, A:V.46, A:T.99, A:S.100 Water bridges: A:R.41, A:S.47, A:R.132, A:K.134, A:K.134, A:K.134 Salt bridges: A:K.112 pi-Stacking: A:F.18 T3P.4: 14 residues within 4Å: Chain B: N.10, M.11, D.12, F.18, F.44, W.45, V.46, W.65, T.99, S.100, P.101, I.102, K.112 Ligands: MG.3 21 PLIP interactions: 21 interactions with chain B Hydrophobic interactions: B:F.44, B:W.45, B:W.45, B:W.65 Hydrogen bonds: B:N.10, B:N.10, B:M.11, B:D.12, B:D.12, B:F.44, B:V.46, B:S.100 Water bridges: B:E.19, B:R.41, B:S.47, B:R.132, B:K.134, B:K.134, B:K.134 Salt bridges: B:K.112 pi-Stacking: B:F.18

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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