SMTL ID : 4l6c.1

Crystal structure of human mitochondrial deoxyribonucleotidase in complex with the inhibitor pib-t

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 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.1, H2O.1 MG.13: 5 residues within 4Å: Chain B: D.15, D.17, D.149, D.150 Ligands: PO4.14 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.15, B:D.17, B:D.150, H2O.8, H2O.8

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

PO4.2: 9 residues within 4Å: Chain A: D.15, M.16, D.17, T.104, S.105, K.117, K.139 Ligands: MG.1, 0BT.3 12 PLIP interactions: 12 interactions with chain A Hydrogen bonds: A:D.15, A:D.15, A:M.16, 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 PO4.14: 9 residues within 4Å: Chain B: D.15, M.16, D.17, T.104, S.105, K.117, K.139 Ligands: MG.13, 0BT.15 12 PLIP interactions: 12 interactions with chain B Hydrogen bonds: B:D.15, B:D.15, B:M.16, 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

2 x 0BT: 1-{2-deoxy-3,5-O-[(4-iodophenyl)(phosphono)methylidene]-beta-D-threo-pentofuranosyl}-5-methylpyrimidine-2,4(1H,3H)-dione(Non-covalent)

0BT.3: 9 residues within 4Å: Chain A: F.23, F.49, W.50, V.51, W.70, I.107, K.108, R.137 Ligands: PO4.2 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:W.50, A:W.50, A:W.70, A:I.107 Hydrogen bonds: A:F.49, A:V.51, A:K.108, A:R.137, A:R.137 Water bridges: A:S.52, A:M.109 pi-Stacking: A:F.23, A:W.50 pi-Cation interactions: A:R.137 Halogen bonds: A:R.137 0BT.15: 9 residues within 4Å: Chain B: F.23, F.49, W.50, V.51, W.70, I.107, K.108, R.137 Ligands: PO4.14 15 PLIP interactions: 15 interactions with chain B Hydrophobic interactions: B:W.50, B:W.50, B:W.70, B:I.107 Hydrogen bonds: B:F.49, B:V.51, B:K.108, B:R.137, B:R.137 Water bridges: B:S.52, B:M.109 pi-Stacking: B:F.23, B:W.50 pi-Cation interactions: B:R.137 Halogen bonds: B:R.137

14 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 7 residues within 4Å: Chain A: R.47, G.48, H.172, N.173, Q.174, H.175, L.176 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:G.48, A:H.172, A:H.175, A:L.176 Water bridges: A:Q.174, A:Q.174 GOL.5: 8 residues within 4Å: Chain A: S.1, N.2, A.93, T.98, D.99, V.100, Q.132 Ligands: GOL.9 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.99, A:V.100 Water bridges: A:N.2, A:N.2 GOL.6: 4 residues within 4Å: Chain A: W.50, R.151, P.152, D.153 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.151, A:D.153, A:D.153, A:D.153 GOL.7: 6 residues within 4Å: Chain A: W.188, A.189, D.190, D.191, W.192, K.193 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:W.188, A:D.191, A:W.192, A:K.193 GOL.8: 5 residues within 4Å: Chain A: G.18, D.22, L.43, A.170, C.171 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.18, A:C.171 Water bridges: A:D.22 GOL.9: 6 residues within 4Å: Chain A: A.93, D.128, F.129, E.131, Q.132 Ligands: GOL.5 2 PLIP interactions: 2 interactions with chain A Water bridges: A:F.129, A:Q.132 GOL.10: 5 residues within 4Å: Chain A: R.11, A.144, D.145, S.162 Chain B: E.158 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.11, A:S.162 Water bridges: A:R.11 GOL.16: 7 residues within 4Å: Chain B: R.47, G.48, H.172, N.173, Q.174, H.175, L.176 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:G.48, B:H.172, B:H.175, B:L.176 Water bridges: B:Q.174, B:Q.174 GOL.17: 8 residues within 4Å: Chain B: S.1, N.2, A.93, T.98, D.99, V.100, Q.132 Ligands: GOL.21 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:S.1, B:D.99, B:D.99, B:V.100 Water bridges: B:N.2, B:N.2 GOL.18: 4 residues within 4Å: Chain B: W.50, R.151, P.152, D.153 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.151, B:D.153, B:D.153 GOL.19: 6 residues within 4Å: Chain B: W.188, A.189, D.190, D.191, W.192, K.193 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:W.188, B:W.192, B:K.193 GOL.20: 5 residues within 4Å: Chain B: G.18, D.22, L.43, A.170, C.171 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:G.18, B:C.171 GOL.21: 6 residues within 4Å: Chain B: A.93, D.128, F.129, E.131, Q.132 Ligands: GOL.17 2 PLIP interactions: 2 interactions with chain B Water bridges: B:F.129, B:Q.132 GOL.22: 5 residues within 4Å: Chain A: E.158 Chain B: R.11, A.144, D.145, S.162 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.11, B:S.162 Water bridges: B:R.11

4 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.11: 2 residues within 4Å: Chain A: P.39, F.40 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:F.40 Water bridges: A:F.40, A:D.45 EDO.12: 8 residues within 4Å: Chain A: N.2, A.3, G.7, R.8, A.9, D.99 Chain B: A.157, P.159 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:N.2, A:A.3, A:A.9 Water bridges: A:A.3, A:A.9, A:R.11 EDO.23: 2 residues within 4Å: Chain B: P.39, F.40 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:F.40 Water bridges: B:F.40, B:D.45 EDO.24: 8 residues within 4Å: Chain A: A.157, P.159 Chain B: N.2, A.3, G.7, R.8, A.9, D.99 6 PLIP interactions: 5 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:N.2, B:A.3, B:A.9 Water bridges: B:A.3, B:R.11, A:A.157

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Simak, O. et al., Conformationally constrained nucleoside phosphonic acids - potent inhibitors of human mitochondrial and cytosolic 5'(3')-nucleotidases. Org.Biomol.Chem. (2014)

Release Date

2014-09-10

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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