MolNFT v1 · #167032 · protein
Structure of DNA polymerase zeta (apo)
6V8P · DNA polymerase zeta catalytic subunit: “Structure of DNA polymerase zeta (apo)”. Electron microscopy, 1 ligand (SF4), 20 pockets (best druggability 0.86). MolNFT v1 #167032 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 6V8P
- Type
- protein
- Length
- 2,117 residues
- Chains
- 5
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA polymerase zeta catalytic subunit; DNA polymerase zeta processivity subunit; DNA…
- EC
- 2.7.7.7
- UniProt
- P14284, P38927, P46957, P47110
- Ligands
- SF4
- Pockets
- 20 · best druggability 0.86
Structure
electron microscopy · 5 distinct chains · 33% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA polymerase zeta catalytic subunit (EC 2.7.7.7) | protein | 1190 | 36% helix, 15% strand | P14284 |
| D | DNA polymerase zeta processivity subunit | protein | 157 | 34% helix, 22% strand | P38927 |
| E | DNA polymerase zeta processivity subunit | protein | 197 | 35% helix, 29% strand | P38927 |
| F | DNA polymerase delta small subunit (EC 2.7.7.7) | protein | 460 | 25% helix, 20% strand | P46957 |
| G | DNA polymerase delta subunit 3 | protein | 113 | 28% helix, 19% strand | P47110 |
Ligands and binding sites
- SF4 · Iron/sulfur cluster · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1118 | 0.86 | 0.87 | 124 | empty |
| 2 | 1073 | 0.85 | 0.86 | 145 | empty |
| 3 | 616 | 0.84 | 0.88 | 101 | empty |
| 4 | 656 | 0.80 | 0.85 | 88 | empty |
| 5 | 985 | 0.80 | 0.81 | 115 | empty |
Interfaces
7 interfaces between chains.
- A–D · 1904 Ų buried · 12 hydrogen bonds · protein-protein
- A–E · 1669 Ų buried · 18 hydrogen bonds · protein-protein
- F–G · 1623 Ų buried · 8 hydrogen bonds · protein-protein
- A–F · 1563 Ų buried · 5 hydrogen bonds · protein-protein
- D–E · 344 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 6V8P · Structure of DNA Polymerase Zeta (Apo) · the same entry in another collection · chain G against G, TM-score 1.00
- P14284 · AlphaFold monomer V2.0 prediction for DNA polymerase zeta catalytic subunit (P14284) · a predicted model of the same protein · chain A against A, TM-score 0.96
- P38927 · AlphaFold monomer V2.0 prediction for DNA polymerase zeta processivity subunit (P38927) · a predicted model of the same protein · chain D against A, TM-score 0.95
- P46957 · AlphaFold monomer V2.0 prediction for DNA polymerase delta small subunit (P46957) · a predicted model of the same protein · chain F against A, TM-score 0.85
- P47110 · AlphaFold monomer V2.0 prediction for DNA polymerase delta subunit 3 (P47110) · a predicted model of the same protein · chain G against A, TM-score 0.81
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 P14284
- Every structure of UniProt P38927
- Every structure of UniProt P46957
- Every structure of UniProt P47110
- Elsewhere: RCSB PDB 6V8P · PDBe 6V8P · UniProt P14284 · UniProt P38927 · UniProt P46957 · UniProt P47110
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