Research workbench
Structure of DNA polymerase zeta with mismatched DNA
Analyse Structure of DNA polymerase zeta with mismatched DNA in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7S0T
- Type
- protein + DNA
- Length
- 2,203 residues
- Chains
- 7
- 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, A0A6A5PTG9, P47110
- Ligands
- SF4, DCP, CA
- Pockets
- 20 · best druggability 0.81
Structure
electron microscopy · 7 distinct chains · 34% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA polymerase zeta catalytic subunit (EC 2.7.7.7) | protein | 1231 | 38% helix, 15% strand | P14284 |
| D | DNA polymerase zeta processivity subunit | protein | 161 | 35% helix, 27% strand | P38927 |
| E | DNA polymerase zeta processivity subunit | protein | 204 | 35% helix, 27% strand | P38927 |
| F | DNA polymerase delta small subunit | protein | 466 | 24% helix, 22% strand | A0A6A5PTG9 |
| G | DNA polymerase delta subunit 3 | protein | 117 | 30% helix, 21% strand | P47110 |
| P | DNA (30-mer) | dna | 10 | — | — |
| T | DNA (30-mer) | dna | 14 | — | — |
Ligands and binding sites
- SF4 · Iron/sulfur cluster · ligand · chains A, F
- DCP · 2'-deoxycytidine-5'-triphosphate · ligand · chains A, P, T
- CA · Calcium ion · metal · 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, 18 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 462 | 0.81 | 0.88 | 52 | empty |
| 2 | 812 | 0.79 | 0.82 | 79 | empty |
| 3 | 1197 | 0.78 | 0.80 | 83 | empty |
| 4 | 955 | 0.74 | 0.77 | 98 | DCP |
| 5 | 566 | 0.74 | 0.81 | 70 | empty |
Interfaces
10 interfaces between chains.
- F–G · 2795 Ų buried · 28 hydrogen bonds · protein-protein
- A–D · 2567 Ų buried · 27 hydrogen bonds · protein-protein
- A–F · 2271 Ų buried · 9 hydrogen bonds · protein-protein
- A–E · 1977 Ų buried · 18 hydrogen bonds · protein-protein
- A–T · 1176 Ų buried · 12 hydrogen bonds · protein-nucleic
Compared structures
- 7S0T · Structure of DNA polymerase zeta with mismatched DNA · the same entry in another collection · chain T against T, 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 0.97
- 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 0.96
- 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 A0A6A5PTG9
- Every structure of UniProt P47110
- Elsewhere: RCSB PDB 7S0T · PDBe 7S0T · UniProt P14284 · UniProt P38927 · UniProt A0A6A5PTG9 · UniProt P47110
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