MolNFT v1 · #50107 · protein + DNA
Structure of the eukaryotic DNA polymerase eta in complex with 1,2- D(GPG)-cisplatin containing DNA
2R8J: “Structure of the eukaryotic DNA polymerase eta in complex with 1,2- D(GPG)-cisplatin containing DNA”. X-ray diffraction, 3 ligands (CPT, DCP, CA), 10 pockets (best druggability 0.79). MolNFT v1 #50107 on GenesisL1: 3D structure…
- PDB
- 2R8J
- 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; DNA (5'-D(*DGP*DTP*DGP*DGP*DAP*DTP*DGP*DAP*DG)-3'); DNA…
- EC
- 2.7.7.7
- UniProt
- Q04049
- Ligands
- CPT, DCP, CA
- Pockets
- 10 · best druggability 0.79
Structure
x-ray diffraction · 4 distinct chains · 40% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA polymerase eta (EC 2.7.7.7) | protein | 511 | 40% helix, 16% strand | Q04049 |
| Q, P | DNA (5'-D(*DGP*DTP*DGP*DGP*DAP*DTP*DGP*DAP*DG)-3') | dna | 9 | — | — |
| U, T | DNA (5'-D(P*DGP*DGP*DCP*DTP*DCP*DAP*DTP*DCP*DCP*DAP*DC)- 3') | dna | 11 | — | — |
| B | DNA polymerase eta (EC 2.7.7.7) | protein | 509 | 40% helix, 17% strand | Q04049 |
Ligands and binding sites
- CPT · Cisplatin · ligand · 2 copies · chains Q, U, P, T
- DCP · 2'-deoxycytidine-5'-triphosphate · ligand · 2 copies · chains A, Q, U, B, P, T
- CA · Calcium ion · metal · 4 copies · chains A, Q, 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 | 1169 | 0.79 | 0.81 | 87 | CA, DCP |
| 2 | 662 | 0.79 | 0.84 | 57 | CA, DCP |
| 3 | 984 | 0.78 | 0.80 | 83 | empty |
| 4 | 298 | 0.63 | 0.81 | 32 | empty |
| 5 | 410 | 0.63 | 0.78 | 32 | empty |
Interfaces
7 interfaces between chains.
- A–B · 1276 Ų buried · 10 hydrogen bonds · protein-protein
- B–T · 592 Ų buried · 12 hydrogen bonds · protein-nucleic
- A–U · 513 Ų buried · 6 hydrogen bonds · protein-nucleic
- P–T · 424 Ų buried · 45 hydrogen bonds · nucleic-nucleic
- Q–U · 423 Ų buried · 28 hydrogen bonds · nucleic-nucleic
Compared structures
- 2R8J · Structure of the Eukaryotic DNA Polymerase eta in complex with 1,2-d(GpG)-cisplatin… · 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 2R8J · PDBe 2R8J · UniProt Q04049
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