SMTL ID : 4mum.1

Crystal structure of mitochondrial 5'(3')-deoxy ribonucleotidase alternative spliced variant

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.27 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.16: 5 residues within 4Å: Chain B: D.15, D.17, D.149, D.150 Ligands: PO4.17 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.15, B:D.17, B:D.150, H2O.12, H2O.12

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, TRS.14 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:S.105, A:K.117 Salt bridges: A:K.117, A:K.139 PO4.17: 10 residues within 4Å: Chain B: D.15, M.16, D.17, T.104, S.105, K.117, K.139 Ligands: MG.16, GOL.18, TRS.29 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:S.105, B:K.117 Salt bridges: B:K.117, B:K.139

16 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 8 residues within 4Å: Chain A: D.17, F.23, E.24, F.49, H.178 Ligands: PO4.2, GOL.5, TRS.14 Ligand excluded by PLIP GOL.4: 1 residues within 4Å: Ligands: PEG.11 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.6, TRS.14 Ligand excluded by PLIP GOL.6: 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.7: 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.8: 7 residues within 4Å: Chain A: D.22, G.25, G.26, R.29, E.80 Ligands: PG4.13, CL.15 Ligand excluded by PLIP GOL.9: 7 residues within 4Å: Chain A: G.84, E.87, A.88, W.194, A.195, D.196, W.198 Ligand excluded by PLIP GOL.10: 6 residues within 4Å: Chain A: G.18, D.22, E.24, L.43, A.176, C.177 Ligand excluded by PLIP GOL.18: 8 residues within 4Å: Chain B: D.17, F.23, E.24, F.49, H.178 Ligands: PO4.17, GOL.20, TRS.29 Ligand excluded by PLIP GOL.19: 1 residues within 4Å: Ligands: PEG.26 Ligand excluded by PLIP GOL.20: 9 residues within 4Å: Chain B: F.23, F.49, W.50, V.51, W.70, I.107 Ligands: GOL.18, GOL.21, TRS.29 Ligand excluded by PLIP GOL.21: 7 residues within 4Å: Chain B: I.67, W.70, E.71, I.107, K.108, M.109 Ligands: GOL.20 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: 7 residues within 4Å: Chain B: D.22, G.25, G.26, R.29, E.80 Ligands: PG4.28, CL.30 Ligand excluded by PLIP GOL.24: 7 residues within 4Å: Chain B: G.84, E.87, A.88, W.194, A.195, D.196, W.198 Ligand excluded by PLIP GOL.25: 6 residues within 4Å: Chain B: G.18, D.22, E.24, L.43, A.176, C.177 Ligand excluded by PLIP

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

PEG.11: 4 residues within 4Å: Chain A: P.187, R.188, R.189 Ligands: GOL.4 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:P.187 PEG.12: 6 residues within 4Å: Chain A: P.106, I.107, K.108, R.137 Chain B: Y.118, L.130 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.108, A:R.137 PEG.26: 4 residues within 4Å: Chain B: P.187, R.188, R.189 Ligands: GOL.19 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:P.187 PEG.27: 6 residues within 4Å: Chain A: Y.118, L.130 Chain B: P.106, I.107, K.108, R.137 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.108, B:R.137

2 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)

PG4.13: 5 residues within 4Å: Chain A: D.22, P.81, L.82, P.83 Ligands: GOL.8 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:P.81 PG4.28: 5 residues within 4Å: Chain B: D.22, P.81, L.82, P.83 Ligands: GOL.23 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:P.81

2 x TRS: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-functional Binders)

TRS.14: 11 residues within 4Å: Chain A: D.17, F.23, F.49, F.76, S.105, P.106, I.107, R.137 Ligands: PO4.2, GOL.3, GOL.5 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:D.17, A:D.17, A:R.137 Water bridges: A:S.105, A:R.137, A:R.151 TRS.29: 11 residues within 4Å: Chain B: D.17, F.23, F.49, F.76, S.105, P.106, I.107, R.137 Ligands: PO4.17, GOL.18, GOL.20 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:D.17, B:R.137 Water bridges: B:S.105, B:R.137, B:R.151

2 x CL: CHLORIDE ION(Non-functional Binders)

CL.15: 5 residues within 4Å: Chain A: D.22, G.26, L.79, E.80 Ligands: GOL.8 Ligand excluded by PLIP CL.30: 5 residues within 4Å: Chain B: D.22, G.26, L.79, E.80 Ligands: GOL.23 Ligand excluded by PLIP

Links

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Citation

Pachl, P. et al., Kinetic and structural characterization of an alternatively spliced variant of human mitochondrial 5'(3')-deoxyribonucleotidase. J Enzyme Inhib Med Chem (2015)

Release Date

2014-02-26

Peptides

Mitochondrial 5' nucleotidase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Mitochondrial 5' nucleotidase