- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.90 Å
- Oligo State
- monomer
- Ligands
- 1 x XJS: 2'-deoxy-5-[9-(3-{[4-(diethylamino)-4-oxobutanoyl]amino}propyl)-18-ethyl-5,8,14,17-tetraoxo-4,9,13,18-tetraazaicos-1-yn-1-yl]uridine 5'-(tetrahydrogen triphosphate)(Non-covalent)
- 8 x GOL: GLYCEROL(Non-functional Binders)
GOL.2: 9 residues within 4Å:- Chain A: N.193, S.194, R.195, D.196, K.219
- Chain C: G.11, T.12, G.13
- Ligands: GOL.6
4 PLIP interactions:4 interactions with chain A- Hydrogen bonds: A:N.193, A:R.195, A:D.196, A:D.196
GOL.3: 6 residues within 4Å:- Chain A: D.160, Y.163, R.304, A.305, I.307, D.534
2 PLIP interactions:2 interactions with chain A- Hydrogen bonds: A:D.160, A:D.534
GOL.4: 4 residues within 4Å:- Chain A: R.21, W.26, D.259, L.260
4 PLIP interactions:4 interactions with chain A- Hydrogen bonds: A:R.21, A:R.21
- Water bridges: A:E.23, A:E.23
GOL.5: 13 residues within 4Å:- Chain A: T.252, Y.253, P.256, L.257, L.260, P.287, N.288, L.289, N.291, I.292
- Chain C: C.9, C.10
- Ligands: PGE.16
2 PLIP interactions:2 interactions with chain A- Hydrogen bonds: A:N.288, A:N.291
GOL.6: 9 residues within 4Å:- Chain A: N.193, S.194, R.195, R.244, K.248
- Chain B: G.7, G.8, C.9
- Ligands: GOL.2
6 PLIP interactions:6 interactions with chain A- Hydrogen bonds: A:R.195
- Water bridges: A:L.192, A:N.193, A:N.193, A:R.244, A:R.244
GOL.15: 7 residues within 4Å:- Chain B: C.6, G.7, G.8, C.9
- Chain C: G.8, C.9, C.10
No protein-ligand interaction detected (PLIP)GOL.17: 5 residues within 4Å:- Chain C: G.5, G.6, C.7
- Ligands: XJS.1, GOL.18
No protein-ligand interaction detected (PLIP)GOL.18: 6 residues within 4Å:- Chain A: A.278, R.436, M.455
- Chain C: G.6, C.7
- Ligands: GOL.17
1 PLIP interactions:1 interactions with chain A- Water bridges: A:A.278
- 2 x MG: MAGNESIUM ION(Non-covalent)
MG.7: 8 residues within 4Å:- Chain A: D.318, Y.319, S.320, Q.321, I.322, D.493
- Ligands: XJS.1, MG.8
3 PLIP interactions:3 interactions with chain A- Metal complexes: A:D.318, A:Y.319, A:D.493
MG.8: 6 residues within 4Å:- Chain A: D.318, D.493, E.494
- Chain B: C.12
- Ligands: XJS.1, MG.7
4 PLIP interactions:2 interactions with chain A, 2 Ligand-Water interactions- Metal complexes: A:D.318, A:D.493, H2O.8, H2O.11
- 4 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)
PGE.9: 6 residues within 4Å:- Chain A: E.170, V.171, E.174, L.246, L.298, R.301
2 PLIP interactions:2 interactions with chain A- Hydrogen bonds: A:R.301, A:R.301
PGE.11: 6 residues within 4Å:- Chain A: L.419, E.450, E.453, R.454, F.457
- Chain C: A.3
3 PLIP interactions:3 interactions with chain A- Hydrogen bonds: A:E.453, A:E.453, A:R.454
PGE.12: 8 residues within 4Å:- Chain A: F.17, V.18, L.19, R.21, K.22, L.60, W.106, R.113
4 PLIP interactions:4 interactions with chain A- Hydrogen bonds: A:L.19, A:L.19, A:R.113, A:R.113
PGE.16: 6 residues within 4Å:- Chain A: D.286, P.287, N.288
- Chain C: C.9, C.10
- Ligands: GOL.5
2 PLIP interactions:2 interactions with chain A- Hydrogen bonds: A:D.286
- Water bridges: A:K.22
- 3 x ACT: ACETATE ION(Non-functional Binders)
ACT.10: 4 residues within 4Å:- Chain A: R.133, W.136, F.432, Y.519
3 PLIP interactions:3 interactions with chain A- Water bridges: A:R.133, A:L.431
- Salt bridges: A:R.133
ACT.13: 4 residues within 4Å:- Chain A: D.160, A.162, Y.163, A.166
3 PLIP interactions:3 interactions with chain A- Hydrophobic interactions: A:Y.163
- Water bridges: A:D.160, A:D.160
ACT.14: 5 residues within 4Å:- Chain A: D.79, F.121, W.125, R.139, R.143
3 PLIP interactions:3 interactions with chain A- Hydrophobic interactions: A:W.125
- Salt bridges: A:R.139, A:R.143
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Obeid, S. et al., Structural basis for the synthesis of nucleobase modified DNA by Thermus aquaticus DNA polymerase. Proc.Natl.Acad.Sci.USA (2010)
- Release Date
- 2010-12-15
- Peptides
- DNA polymerase I, thermostable: A
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
A
- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.90 Å
- Oligo State
- monomer
- Ligands
- 1 x XJS: 2'-deoxy-5-[9-(3-{[4-(diethylamino)-4-oxobutanoyl]amino}propyl)-18-ethyl-5,8,14,17-tetraoxo-4,9,13,18-tetraazaicos-1-yn-1-yl]uridine 5'-(tetrahydrogen triphosphate)(Non-covalent)
- 8 x GOL: GLYCEROL(Non-functional Binders)
- 2 x MG: MAGNESIUM ION(Non-covalent)
- 4 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)
- 3 x ACT: ACETATE ION(Non-functional Binders)
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Obeid, S. et al., Structural basis for the synthesis of nucleobase modified DNA by Thermus aquaticus DNA polymerase. Proc.Natl.Acad.Sci.USA (2010)
- Release Date
- 2010-12-15
- Peptides
- DNA polymerase I, thermostable: A
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
A