- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.15 Å
- Oligo State
- monomer
- Ligands
- 1 x DT- DG- DC- DG- DT- DC- DA- DT- DA: DNA (5'-D(*TP*GP*CP*GP*TP*CP*AP*TP*A)-3')(Non-covalent)
- 1 x DZ4: 2'-deoxy-5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]adenosine(Non-covalent)
DZ4.2: 17 residues within 4Å:- Chain A: D.16, M.17, D.18, C.19, F.20, F.21, I.51, A.52, Y.55, R.58, R.64, D.118, K.234
- Chain B: T.5
- Ligands: DT-DG-DC-DG-DT-DC-DA-DT-DA.1, MG.19, MG.20
11 PLIP interactions:11 interactions with chain A- Hydrophobic interactions: A:F.21
- Hydrogen bonds: A:M.17, A:C.19, A:F.20, A:F.21, A:Y.55, A:R.64
- Water bridges: A:D.16, A:D.16
- Salt bridges: A:R.58, A:K.234
- 8 x GOL: GLYCEROL(Non-functional Binders)
GOL.3: 4 residues within 4Å:- Chain A: H.243, G.244, P.247
- Ligands: EDO.18
1 PLIP interactions:1 interactions with chain A- Hydrogen bonds: A:H.243
GOL.4: 2 residues within 4Å:- Chain A: T.285, S.287
1 PLIP interactions:1 interactions with chain A- Water bridges: A:E.286
GOL.5: 2 residues within 4Å:- Chain A: T.356, N.360
1 PLIP interactions:1 interactions with chain A- Hydrogen bonds: A:N.360
GOL.6: 8 residues within 4Å:- Chain A: L.14, D.16, E.119, K.227, C.230, G.231, K.234
- Ligands: DT-DG-DC-DG-DT-DC-DA-DT-DA.1
3 PLIP interactions:3 interactions with chain A- Hydrogen bonds: A:E.119, A:K.227, A:K.227
GOL.8: 3 residues within 4Å:- Chain A: Q.283, F.284, Q.288
2 PLIP interactions:2 interactions with chain A- Hydrogen bonds: A:Q.283, A:Q.288
GOL.9: 3 residues within 4Å:- Chain A: V.375, D.378, R.380
1 PLIP interactions:1 interactions with chain A- Hydrogen bonds: A:R.380
GOL.10: 3 residues within 4Å:- Chain A: D.143, E.167, K.171
3 PLIP interactions:3 interactions with chain A- Hydrogen bonds: A:D.143, A:E.167, A:K.171
GOL.11: 5 residues within 4Å:- Chain A: L.265, S.268, H.292, F.293
- Ligands: EDO.16
3 PLIP interactions:3 interactions with chain A- Hydrogen bonds: A:S.268, A:S.268
- Water bridges: A:F.293
- 1 x 3D1: (2R,3S,5R)-5-(6-amino-9H-purin-9-yl)-tetrahydro-2-(hydroxymethyl)furan-3-ol(Non-covalent)
- 2 x DTT: 2,3-DIHYDROXY-1,4-DITHIOBUTANE(Non-covalent)
DTT.12: 3 residues within 4Å:- Chain A: Q.290, G.294, E.295
1 PLIP interactions:1 interactions with chain A- Hydrogen bonds: A:Q.290
DTT.13: 9 residues within 4Å:- Chain A: E.151, G.152, Q.155, W.177, D.190, S.242, G.244, S.245
- Ligands: EDO.14
2 PLIP interactions:2 interactions with chain A- Hydrogen bonds: A:E.151
- Water bridges: A:S.245
- 5 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)
EDO.14: 3 residues within 4Å:- Chain A: Q.155, S.180
- Ligands: DTT.13
2 PLIP interactions:2 interactions with chain A- Hydrogen bonds: A:Q.155
- Water bridges: A:W.177
EDO.15: 8 residues within 4Å:- Chain A: K.227, R.256, K.257, I.258, R.259, G.262
- Ligands: DT-DG-DC-DG-DT-DC-DA-DT-DA.1, DT-DG-DC-DG-DT-DC-DA-DT-DA.1
2 PLIP interactions:2 interactions with chain A- Hydrogen bonds: A:K.227
- Water bridges: A:R.259
EDO.16: 2 residues within 4Å:- Chain A: L.265
- Ligands: GOL.11
No protein-ligand interaction detected (PLIP)EDO.17: 3 residues within 4Å:- Chain A: R.256, G.263, K.264
1 PLIP interactions:1 interactions with chain A- Hydrogen bonds: A:R.256
EDO.18: 3 residues within 4Å:- Chain A: H.243, R.306
- Ligands: GOL.3
No protein-ligand interaction detected (PLIP)- 2 x MG: MAGNESIUM ION(Non-covalent)
MG.19: 5 residues within 4Å:- Chain A: D.16, M.17, D.118
- Ligands: DZ4.2, MG.20
3 PLIP interactions:3 interactions with chain A- Metal complexes: A:D.16, A:M.17, A:D.118
MG.20: 7 residues within 4Å:- Chain A: D.16, S.116, D.118, E.119
- Ligands: DT-DG-DC-DG-DT-DC-DA-DT-DA.1, DZ4.2, MG.19
4 PLIP interactions:3 interactions with chain A, 1 Ligand-Water interactions- Metal complexes: A:D.16, A:D.118, A:E.119, H2O.2
- 1 x CO: COBALT (II) ION(Non-covalent)
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Biertumpfel, C. et al., Structure and mechanism of human DNA polymerase eta. Nature (2010)
- Release Date
- 2011-08-03
- Peptides
- DNA polymerase eta: A
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
A
SMTL ID : 3si8.1
Human DNA polymerase eta - DNA ternary complex with the 5'T of a CPD in the active site (TT2)
DNA polymerase eta
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3jaa.1 | 3mr2.1 | 3mr3.1 | 3mr5.1 | 4dl2.1 | 4dl3.1 | 4dl4.1 | 4dl5.1 | 4dl6.1 | 4dl7.1 | 4ecq.1 | 4ecr.1 | 4ecs.1 | 4ect.1 | 4ecu.1 | 4ecv.1 | 4ecw.1 | 4ecx.1 | 4ecy.1 | 4ecz.1 | 4ed0.1 | 4ed1.1 | 4ed2.1 | 4ed3.1 | 4ed6.1 | 4ed7.1 | 4ed8.1 | 4j9k.1 | 4j9l.1 | 4j9m.1 more...less...4j9n.1 | 4j9o.1 | 4j9p.1 | 4j9q.1 | 4j9r.1 | 4j9s.1 | 4o3n.1 | 4o3o.1 | 4o3p.1 | 4o3q.1 | 4o3r.1 | 4q8e.1 | 4q8f.1 | 4rnm.1 | 4rnn.1 | 4rno.1 | 5dg7.1 | 5dg8.1 | 5dg9.1 | 5dga.1 | 5dgb.1 | 5dlf.1 | 5dlg.1 | 5dqg.1 | 5dqh.1 | 5dqi.1 | 5ewe.1 | 5ewf.1 | 5ewg.1 | 5f9l.1 | 5f9n.1 | 5jum.1 | 5kfa.1 | 5kfb.1 | 5kfc.1 | 5kfd.1 | 5kfe.1 | 5kff.1 | 5kfg.1 | 5kfh.1 | 5kfi.1 | 5kfj.1 | 5kfk.1 | 5kfl.1 | 5kfm.1 | 5kfn.1 | 5kfo.1 | 5kfp.1 | 5kfq.1 | 5kfr.1 | 5kfy.1 | 5kfz.1 | 5kg0.1 | 5kg1.1 | 5kg2.1 | 5kg3.1 | 5kg4.1 | 5kg5.1 | 5kg6.1 | 5kg7.1 | 5l1i.1 | 5l1j.1 | 5l1k.1 | 5l1l.1 | 5l9x.1 | 6m7o.1 | 6m7p.1 | 6m7t.1 | 6m7u.1 | 6m7v.1 | 6mp3.1 | 6pl7.1 | 6pl8.1 | 6plc.1 | 6ui2.1 | 7m7l.1 | 7m7m.1 | 7m7n.1 | 7m7o.1 | 7m7y.1 | 7m7z.1 | 7m80.1 | 7m81.1 | 7m82.1 | 7u72.1 | 7u73.1 | 7u74.1 | 7u75.1 | 7u76.1 | 7u77.1 | 7u78.1 | 7u79.1 | 7u7a.1 | 7u7b.1 | 7u7c.1 | 7u7d.1 | 7u7e.1 | 7u7f.1 | 7u7g.1 | 7u7i.1 | 7u7j.1 | 7u7k.1 | 7u7l.1 | 7u7r.1 | 7u7s.1 | 7u7t.1 | 7u7u.1 | 7u7v.1 | 7u7w.1 | 7u7x.1 | 7u7y.1 | 7u7z.1 | 7u80.1 | 7u81.1 | 7u82.1 | 7u83.1 | 7u84.1 | 8e85.1 | 8e86.1 | 8e87.1 | 8e88.1 | 8e89.1 | 8e8a.1 | 8e8b.1 | 8e8c.1 | 8e8d.1 | 8e8e.1 | 8e8f.1 | 8e8g.1 | 8e8h.1 | 8e8j.1 | 8e8k.1 | 8eve.1 | 8evf.1 | 8ujt.1 | 8ujv.1 | 8ujx.1 | 8uk4.1 | 8v7a.1 | 8v7b.1 | 8v7c.1 | 8v7d.1 | 8v7e.1 | 8v7f.1 | 8v7g.1 | 8v7h.1 | 8v7i.1 | 8v7j.1 | 8v7k.1 | 9chw.1 | 9ci9.1 | 9cih.1 | 9ciq.1 | 9cj9.1