- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.27 Å
- Oligo State
- homo-dimer
- Ligands
- 2 x MG: MAGNESIUM ION(Non-covalent)
- 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 PLIPGOL.4: 1 residues within 4Å:- Ligands: PEG.11
Ligand excluded by PLIPGOL.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 PLIPGOL.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 PLIPGOL.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 PLIPGOL.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 PLIPGOL.9: 7 residues within 4Å:- Chain A: G.84, E.87, A.88, W.194, A.195, D.196, W.198
Ligand excluded by PLIPGOL.10: 6 residues within 4Å:- Chain A: G.18, D.22, E.24, L.43, A.176, C.177
Ligand excluded by PLIPGOL.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 PLIPGOL.19: 1 residues within 4Å:- Ligands: PEG.26
Ligand excluded by PLIPGOL.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 PLIPGOL.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 PLIPGOL.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 PLIPGOL.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 PLIPGOL.24: 7 residues within 4Å:- Chain B: G.84, E.87, A.88, W.194, A.195, D.196, W.198
Ligand excluded by PLIPGOL.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)
- 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)
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- 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
AB
A
- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.27 Å
- Oligo State
- homo-dimer
- Ligands
- 2 x MG: MAGNESIUM ION(Non-covalent)
- 2 x PO4: PHOSPHATE ION(Non-functional Binders)
- 16 x GOL: GLYCEROL(Non-functional Binders)
- 4 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)
- 2 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)
- 2 x TRS: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-functional Binders)
- 2 x CL: CHLORIDE ION(Non-functional Binders)
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- 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
AB
A