MolNFT v1 · #167045 · protein + DNA
Structure of DNA polymerase ZETA/DNA/DNTP ternary complex
6V93 · DNA polymerase zeta catalytic subunit: “Structure of DNA polymerase ZETA/DNA/DNTP ternary complex”. Electron microscopy, 3 ligands (SF4, DCP, CA), 20 pockets (best druggability 0.83). MolNFT v1 #167045 on GenesisL1: 3D structure…
- PDB
- 6V93
- Type
- protein + DNA
- Length
- 2,224 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, P46957, P47110
- Ligands
- SF4, DCP, CA
- Pockets
- 20 · best druggability 0.83
Structure
electron microscopy · 7 distinct chains · 32% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA polymerase zeta catalytic subunit (EC 2.7.7.7) | protein | 1259 | 36% helix, 15% strand | P14284 |
| D | DNA polymerase zeta processivity subunit | protein | 159 | 36% helix, 25% strand | P38927 |
| E | DNA polymerase zeta processivity subunit | protein | 202 | 34% helix, 26% strand | P38927 |
| F | DNA polymerase delta small subunit (EC 2.7.7.7) | protein | 461 | 23% helix, 21% strand | P46957 |
| G | DNA polymerase delta subunit 3 | protein | 117 | 27% helix, 22% strand | P47110 |
| P | DNA | dna | 11 | — | — |
| T | DNA | dna | 15 | — | — |
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 · 2 copies · chains A, P
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 17 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1042 | 0.83 | 0.84 | 86 | empty |
| 2 | 962 | 0.78 | 0.80 | 96 | empty |
| 3 | 304 | 0.78 | 0.90 | 34 | empty |
| 4 | 1033 | 0.78 | 0.80 | 96 | CA, DCP |
| 5 | 248 | 0.77 | 0.90 | 46 | empty |
Interfaces
10 interfaces between chains.
- F–G · 2826 Ų buried · 29 hydrogen bonds · protein-protein
- A–F · 2601 Ų buried · 5 hydrogen bonds · protein-protein
- A–D · 2589 Ų buried · 24 hydrogen bonds · protein-protein
- A–E · 1993 Ų buried · 16 hydrogen bonds · protein-protein
- A–T · 1333 Ų buried · 16 hydrogen bonds · protein-nucleic
Compared structures
- 6V93 · Structure of DNA Polymerase Zeta/DNA/dNTP Ternary Complex · 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 0.96
- 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 0.96
- 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 0.86
- 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 6V93 · PDBe 6V93 · UniProt P14284 · UniProt P38927 · UniProt P46957 · UniProt P47110
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