SMTL ID : 4l57.1

High resolutin structure of human cytosolic 5'(3')-deoxyribonucleotidase

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.08 Å

Oligo State

homo-dimer

Ligands

2 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 5 residues within 4Å: Chain A: D.10, D.12, D.144, D.145 Ligands: PO4.2 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.10, A:D.12, A:D.145, H2O.1, H2O.1 MG.9: 5 residues within 4Å: Chain B: D.10, D.12, D.144, D.145 Ligands: PO4.10 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.10, B:D.12, B:D.145, H2O.11, H2O.11

2 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.2: 9 residues within 4Å: Chain A: D.10, M.11, D.12, T.99, S.100, K.112, K.134 Ligands: MG.1, GOL.4 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:M.11, A:D.12, A:D.12, A:D.12, A:D.12, A:T.99, A:S.100 Water bridges: A:S.100, A:K.134 Salt bridges: A:K.112, A:K.134 PO4.10: 9 residues within 4Å: Chain B: D.10, M.11, D.12, T.99, S.100, K.112, K.134 Ligands: MG.9, GOL.11 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:M.11, B:D.12, B:D.12, B:D.12, B:S.100 Water bridges: B:K.134, B:K.134 Salt bridges: B:K.112, B:K.134

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 4 residues within 4Å: Chain A: N.186, W.187, R.188, E.189 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.186, A:N.186, A:E.189 Water bridges: A:R.188, A:R.188 GOL.4: 7 residues within 4Å: Chain A: D.12, F.18, E.19, F.44, H.167 Ligands: PO4.2, GOL.7 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.19, A:E.19, A:F.44 Water bridges: A:D.12 GOL.5: 4 residues within 4Å: Chain A: F.44, S.100, R.132, K.146 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:S.100, A:S.100 Water bridges: A:R.132, A:R.132, A:R.132, A:K.134, A:R.150 GOL.6: 2 residues within 4Å: Chain A: R.51, D.59 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.51 Water bridges: A:R.51, A:P.55, A:P.55, A:D.59 GOL.7: 9 residues within 4Å: Chain A: F.18, E.19, R.41, F.44, L.45, A.46, R.47, Y.65 Ligands: GOL.4 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.41, A:F.44, A:A.46, A:R.47, A:Y.65 GOL.11: 7 residues within 4Å: Chain B: D.12, F.18, F.44, L.45, F.71, L.102 Ligands: PO4.10 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.12 Water bridges: B:L.103

1 x NA: SODIUM ION(Non-functional Binders)

NA.8: 4 residues within 4Å: Chain A: N.88, D.89, L.90, T.93 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.93 Water bridges: A:T.93

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Pachl, P. et al., Structures of human cytosolic and mitochondrial nucleotidases: implications for structure-based design of selective inhibitors. Acta Crystallogr. D Biol. Crystallogr. (2014)

Release Date

2014-02-12

Peptides

5'(3')-deoxyribonucleotidase, cytosolic type: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

5'(3')-deoxyribonucleotidase, cytosolic type

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