Research workbench
DNA polymerase eta in complex with the cis-diammineplatinum (II) 1,3-gtg intrastrand cross-link
Analyse DNA polymerase eta in complex with the cis-diammineplatinum (II) 1,3-gtg… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2WTF
- Type
- protein + DNA
- Length
- 1,061 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA polymerase eta; 5'-D(*TP*CP*TP*TP*CP*TP*GP*TP*GP*CP *TP*CP*AP*CP*CP*AP*CP)-3'…
- EC
- 2.7.7.7
- UniProt
- Q04049
- Ligands
- DTP, CPT, CA
- Pockets
- 10 · best druggability 0.83
Structure
x-ray diffraction · 5 distinct chains · 40% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA polymerase eta (EC 2.7.7.7) | protein | 509 | 40% helix, 19% strand | Q04049 |
| B | DNA polymerase eta (EC 2.7.7.7) | protein | 508 | 40% helix, 18% strand | Q04049 |
| O | 5'-D(*TP*CP*TP*TP*CP*TP*GP*TP*GP*CP *TP*CP*AP*CP*CP*AP*CP)-3' | dna | 14 | — | — |
| P, T | 5'-D(*GP*TP*GP*GP*TP*GP*AP*GP*CP)-3' | dna | 9 | — | — |
| S | 5'-D(*TP*CP*TP*TP*CP*TP*GP*TP*GP*CP *TP*CP*AP*CP*CP*AP*CP)-3' | dna | 12 | — | — |
Ligands and binding sites
- DTP · 2'-deoxyadenosine 5'-triphosphate · ligand · 2 copies · chains A, O, P, B, S, T
- CPT · Cisplatin · ligand · 2 copies · chains O, P, S, T
- CA · Calcium ion · metal · 10 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 994 | 0.83 | 0.84 | 80 | CA, DTP |
| 2 | 1144 | 0.80 | 0.82 | 79 | DTP, CA |
| 3 | 1128 | 0.73 | 0.76 | 80 | empty |
| 4 | 375 | 0.67 | 0.80 | 38 | empty |
| 5 | 467 | 0.65 | 0.78 | 34 | empty |
Interfaces
7 interfaces between chains.
- A–B · 1303 Ų buried · 19 hydrogen bonds · protein-protein
- A–O · 811 Ų buried · 12 hydrogen bonds · protein-nucleic
- B–S · 661 Ų buried · 13 hydrogen bonds · protein-nucleic
- S–T · 425 Ų buried · 44 hydrogen bonds · nucleic-nucleic
- O–P · 418 Ų buried · 39 hydrogen bonds · nucleic-nucleic
Compared structures
- 2WTF · DNA polymerase eta in complex with the cis-diammineplatinum (II) 1,3- GTG intrastrand… · the same entry in another collection · chain T against T, TM-score 1.00
- Q04049 · AlphaFold monomer V2.0 prediction for DNA polymerase eta (Q04049) · a predicted model of the same protein · chain A against A, TM-score 0.92
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt Q04049
- Elsewhere: RCSB PDB 2WTF · PDBe 2WTF · UniProt Q04049
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