MolNFT v1 · #50108 · protein + DNA
Structure of the eukaryotic DNA polymerase eta in complex with 1,2- D(GPG)-cisplatin containing DNA
2R8K: “Structure of the eukaryotic DNA polymerase eta in complex with 1,2- D(GPG)-cisplatin containing DNA”. X-ray diffraction, 3 ligands (CPT, DTP, CA), 14 pockets (best druggability 0.81). MolNFT v1 #50108 on GenesisL1: 3D structure…
- PDB
- 2R8K
- Type
- protein + DNA
- Length
- 1,060 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA polymerase eta; 5'-D(*DGP*DTP*DGP*DGP*DTP*DGP*DAP*DGP*DC)-3'…
- EC
- 2.7.7.7
- UniProt
- Q04049
- Ligands
- CPT, DTP, CA
- Pockets
- 14 · best druggability 0.81
Structure
x-ray diffraction · 3 distinct chains · 36% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | DNA polymerase eta (EC 2.7.7.7) | protein | 511 | 36% helix, 18% strand | Q04049 |
| Q, P | 5'-D(*DGP*DTP*DGP*DGP*DTP*DGP*DAP*DGP*DC)-3' | dna | 9 | — | — |
| U, T | 5'-D(P*DGP*DGP*DCP*DTP*DCP*DAP*DCP*DCP*DAP*DC)-3' | dna | 10 | — | — |
Ligands and binding sites
- CPT · Cisplatin · ligand · 2 copies · chains Q, U, T
- DTP · 2'-deoxyadenosine 5'-triphosphate · ligand · 2 copies · chains A, Q, U, B, P, T
- CA · Calcium ion · metal · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 645 | 0.81 | 0.86 | 57 | CA, DTP |
| 2 | 476 | 0.79 | 0.87 | 34 | empty |
| 3 | 267 | 0.70 | 0.85 | 38 | empty |
| 4 | 497 | 0.68 | 0.79 | 37 | empty |
| 5 | 177 | 0.68 | 0.87 | 25 | empty |
Interfaces
7 interfaces between chains.
- A–B · 1244 Ų buried · 11 hydrogen bonds · protein-protein
- B–T · 614 Ų buried · 13 hydrogen bonds · protein-nucleic
- A–U · 477 Ų buried · 10 hydrogen bonds · protein-nucleic
- Q–U · 396 Ų buried · 29 hydrogen bonds · nucleic-nucleic
- P–T · 383 Ų buried · 24 hydrogen bonds · nucleic-nucleic
Compared structures
- 2R8K · Structure of the Eukaryotic DNA Polymerase eta in complex with 1,2-d(GpG)-cisplatin… · the same entry in another collection · chain U against U, 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 2R8K · PDBe 2R8K · UniProt Q04049
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