- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.00 Å
- Oligo State
- monomer
- Ligands
- 1 x SSJ: 2'-deoxy-5-[(1-hydroxy-2,2,5,5-tetramethyl-2,5-dihydro-1H-pyrrol-3-yl)ethynyl]uridine 5'-(tetrahydrogen triphosphate)(Non-covalent)
- 2 x MG: MAGNESIUM ION(Non-covalent)
MG.2: 7 residues within 4Å:- Chain A: D.318, Y.319, S.320, Q.321, D.493
- Ligands: SSJ.1, MG.3
3 PLIP interactions:3 interactions with chain A- Metal complexes: A:D.318, A:Y.319, A:D.493
MG.3: 7 residues within 4Å:- Chain A: D.318, D.493, E.494, K.539
- Chain B: C.12
- Ligands: SSJ.1, MG.2
2 PLIP interactions:1 interactions with chain A, 1 Ligand-Water interactions- Metal complexes: A:D.318, H2O.1
- 6 x GOL: GLYCEROL(Non-functional Binders)
GOL.4: 8 residues within 4Å:- Chain A: L.60, K.62, D.63, R.271, F.272, N.273, Q.274, T.275
9 PLIP interactions:9 interactions with chain A- Hydrogen bonds: A:K.62, A:D.63, A:D.63, A:N.273, A:Q.274
- Water bridges: A:R.271, A:Q.274, A:T.275, A:T.275
GOL.5: 13 residues within 4Å:- Chain A: T.252, Y.253, P.256, L.257, L.260, D.286, P.287, N.288, L.289, N.291, I.292
- Chain C: C.9, C.10
3 PLIP interactions:3 interactions with chain A- Hydrogen bonds: A:N.288, A:N.291
- Water bridges: A:D.286
GOL.6: 9 residues within 4Å:- Chain A: L.192, N.193, R.195, R.244
- Chain B: G.7, G.8
- Chain C: G.11, T.12
- Ligands: GOL.9
4 PLIP interactions:4 interactions with chain A- Hydrogen bonds: A:R.244
- Water bridges: A:L.192, A:L.192, A:S.194
GOL.9: 9 residues within 4Å:- Chain A: N.193, S.194, R.195, D.196
- Chain B: C.6
- 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.15: 6 residues within 4Å:- Chain A: E.132, R.133, W.136, L.137, F.432, Y.519
4 PLIP interactions:4 interactions with chain A- Hydrogen bonds: A:R.133, A:R.133, A:R.133, A:Y.519
GOL.19: 6 residues within 4Å:- Chain A: A.278, R.436, M.455
- Chain C: G.6, C.7
- Ligands: PGE.20
1 PLIP interactions:1 interactions with chain A- Hydrogen bonds: A:R.436
- 11 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)
PGE.7: 6 residues within 4Å:- Chain A: E.55, R.57, G.78, D.79, R.143
- Ligands: PGE.11
3 PLIP interactions:3 interactions with chain A- Hydrogen bonds: A:R.57, A:D.79
- Water bridges: A:R.143
PGE.8: 6 residues within 4Å:- Chain A: G.380, L.419, E.450, E.453, R.454, F.457
1 PLIP interactions:1 interactions with chain A- Hydrogen bonds: A:R.454
PGE.10: 3 residues within 4Å:- Chain A: K.475, R.479, V.514
3 PLIP interactions:3 interactions with chain A- Hydrogen bonds: A:K.475, A:R.479
- Water bridges: A:G.517
PGE.11: 8 residues within 4Å:- Chain A: R.57, D.79, F.121, W.125, Y.138, R.139, R.143
- Ligands: PGE.7
3 PLIP interactions:3 interactions with chain A- Hydrogen bonds: A:R.57, A:R.143, A:R.143
PGE.12: 6 residues within 4Å:- Chain A: R.21, E.23, W.26, D.259, L.260, D.286
3 PLIP interactions:3 interactions with chain A- Hydrogen bonds: A:R.21, A:R.21
- Water bridges: A:W.26
PGE.13: 7 residues within 4Å:- Chain A: G.104, E.105, T.107, E.112, A.115, L.116, R.119
3 PLIP interactions:3 interactions with chain A- Hydrogen bonds: A:E.105, A:R.119, A:R.119
PGE.14: 5 residues within 4Å:- Chain A: S.168, L.169, A.172, K.250, D.255
2 PLIP interactions:2 interactions with chain A- Hydrogen bonds: A:S.168, A:K.250
PGE.16: 5 residues within 4Å:- Chain A: T.155, T.265, R.267, E.309, R.486
2 PLIP interactions:2 interactions with chain A- Hydrogen bonds: A:R.486, A:R.486
PGE.17: 4 residues within 4Å:- Chain A: R.184, L.185, A.186, G.187
No protein-ligand interaction detected (PLIP)PGE.18: 6 residues within 4Å:- Chain A: R.423, L.441, E.442, A.443, R.444, R.449
3 PLIP interactions:3 interactions with chain A- Hydrogen bonds: A:L.441, A:A.443
- Water bridges: A:R.449
PGE.20: 4 residues within 4Å:- Chain C: G.5, G.6, C.7
- Ligands: GOL.19
No protein-ligand interaction detected (PLIP)- 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 2.00 Å
- Oligo State
- monomer
- Ligands
- 1 x SSJ: 2'-deoxy-5-[(1-hydroxy-2,2,5,5-tetramethyl-2,5-dihydro-1H-pyrrol-3-yl)ethynyl]uridine 5'-(tetrahydrogen triphosphate)(Non-covalent)
- 2 x MG: MAGNESIUM ION(Non-covalent)
- 6 x GOL: GLYCEROL(Non-functional Binders)
- 11 x PGE: TRIETHYLENE GLYCOL(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