SMTL ID : 4l6a.1

Structure of human mitochondrial 5'(3')-deoxyribonucleotidase

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.40 Å

Oligo State

homo-dimer

Ligands

2 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 5 residues within 4Å: Chain A: D.15, D.17, D.149, D.150 Ligands: PO4.2 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.15, A:D.17, A:D.150, H2O.2, H2O.2 MG.17: 5 residues within 4Å: Chain B: D.15, D.17, D.149, D.150 Ligands: PO4.18 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.15, B:D.17, B:D.150, H2O.14, H2O.14

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

PO4.2: 10 residues within 4Å: Chain A: D.15, M.16, D.17, T.104, S.105, K.117, K.139 Ligands: MG.1, GOL.3, GOL.8 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:M.16, A:D.17, A:D.17, A:D.17, A:D.17, A:S.105 Water bridges: A:S.105, A:K.117, A:K.139 Salt bridges: A:K.117, A:K.139 PO4.18: 10 residues within 4Å: Chain B: D.15, M.16, D.17, T.104, S.105, K.117, K.139 Ligands: MG.17, GOL.19, GOL.24 11 PLIP interactions: 11 interactions with chain B Hydrogen bonds: B:M.16, B:D.17, B:D.17, B:D.17, B:T.104, B:S.105 Water bridges: B:S.105, B:K.117, B:K.139 Salt bridges: B:K.117, B:K.139

18 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 8 residues within 4Å: Chain A: D.17, F.23, E.24, F.49, H.172 Ligands: PO4.2, GOL.5, GOL.8 Ligand excluded by PLIP GOL.4: 7 residues within 4Å: Chain A: I.67, W.70, E.71, I.107, K.108, M.109 Ligands: GOL.5 Ligand excluded by PLIP GOL.5: 9 residues within 4Å: Chain A: F.23, F.49, W.50, V.51, W.70, I.107 Ligands: GOL.3, GOL.4, GOL.8 Ligand excluded by PLIP GOL.6: 8 residues within 4Å: Chain A: S.1, N.2, A.93, T.98, D.99, V.100, F.129, Q.132 Ligand excluded by PLIP GOL.7: 5 residues within 4Å: Chain A: R.137, D.138, R.151, T.155, G.156 Ligand excluded by PLIP GOL.8: 9 residues within 4Å: Chain A: D.17, F.49, W.50, S.105, P.106, R.137 Ligands: PO4.2, GOL.3, GOL.5 Ligand excluded by PLIP GOL.9: 3 residues within 4Å: Chain A: I.67, E.71, M.109 Ligand excluded by PLIP GOL.10: 5 residues within 4Å: Chain A: D.191, W.192, K.193 Ligands: PEG.13, PEG.15 Ligand excluded by PLIP GOL.11: 3 residues within 4Å: Chain A: N.74, F.77, Y.115 Ligand excluded by PLIP GOL.19: 8 residues within 4Å: Chain B: D.17, F.23, E.24, F.49, H.172 Ligands: PO4.18, GOL.21, GOL.24 Ligand excluded by PLIP GOL.20: 7 residues within 4Å: Chain B: I.67, W.70, E.71, I.107, K.108, M.109 Ligands: GOL.21 Ligand excluded by PLIP GOL.21: 9 residues within 4Å: Chain B: F.23, F.49, W.50, V.51, W.70, I.107 Ligands: GOL.19, GOL.20, GOL.24 Ligand excluded by PLIP GOL.22: 8 residues within 4Å: Chain B: S.1, N.2, A.93, T.98, D.99, V.100, F.129, Q.132 Ligand excluded by PLIP GOL.23: 5 residues within 4Å: Chain B: R.137, D.138, R.151, T.155, G.156 Ligand excluded by PLIP GOL.24: 9 residues within 4Å: Chain B: D.17, F.49, W.50, S.105, P.106, R.137 Ligands: PO4.18, GOL.19, GOL.21 Ligand excluded by PLIP GOL.25: 3 residues within 4Å: Chain B: I.67, E.71, M.109 Ligand excluded by PLIP GOL.26: 5 residues within 4Å: Chain B: D.191, W.192, K.193 Ligands: PEG.29, PEG.31 Ligand excluded by PLIP GOL.27: 3 residues within 4Å: Chain B: N.74, F.77, Y.115 Ligand excluded by PLIP

8 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.12: 9 residues within 4Å: Chain A: R.46, R.47, G.48, C.171, H.172, N.173, Q.174, H.175, L.176 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.47, A:G.48, A:C.171 Water bridges: A:F.49, A:Q.174 PEG.13: 7 residues within 4Å: Chain A: A.88, E.91, W.188, A.189, D.190, W.192 Ligands: GOL.10 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.91, A:A.189 Water bridges: A:A.88 PEG.14: 3 residues within 4Å: Chain A: P.181, R.182, R.183 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:P.181 Water bridges: A:R.183, A:R.184 PEG.15: 2 residues within 4Å: Chain A: D.191 Ligands: GOL.10 No protein-ligand interaction detected (PLIP) PEG.28: 9 residues within 4Å: Chain B: R.46, R.47, G.48, C.171, H.172, N.173, Q.174, H.175, L.176 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:R.47, B:G.48, B:C.171 Water bridges: B:F.49, B:Q.174 PEG.29: 7 residues within 4Å: Chain B: A.88, E.91, W.188, A.189, D.190, W.192 Ligands: GOL.26 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:A.189 Water bridges: B:A.88 PEG.30: 3 residues within 4Å: Chain B: P.181, R.182, R.183 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:P.181 Water bridges: B:R.183, B:R.184 PEG.31: 2 residues within 4Å: Chain B: D.191 Ligands: GOL.26 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:D.191

2 x K: POTASSIUM ION(Non-covalent)

K.16: 4 residues within 4Å: Chain A: P.152, I.154, H.165, R.182 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:H.165 K.32: 4 residues within 4Å: Chain B: P.152, I.154, H.165, R.182 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:H.165

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, mitochondrial: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

5'(3')-deoxyribonucleotidase, mitochondrial

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