MolNFT v1 · #181521 · protein
Structure of yeast DNA polymerase zeta (apo)
7LXD · DNA polymerase zeta catalytic subunit: “Structure of yeast DNA polymerase zeta (apo)”. Electron microscopy, 1 ligand (SF4), 20 pockets (best druggability 0.74). MolNFT v1 #181521 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 7LXD
- Type
- protein
- Length
- 2,135 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 0.74
Structure
electron microscopy · 5 distinct chains · 32% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA polymerase zeta catalytic subunit (EC 2.7.7.7) | protein | 1190 | 35% helix, 8% strand | P14284 |
| D | DNA polymerase zeta processivity subunit | protein | 163 | 34% helix, 15% strand | P38927 |
| E | DNA polymerase zeta processivity subunit | protein | 205 | 36% helix, 26% strand | P38927 |
| F | DNA polymerase delta small subunit (EC 2.7.7.7) | protein | 459 | 24% helix, 13% strand | P46957 |
| G | DNA polymerase delta subunit 3 | protein | 118 | 27% helix, 8% strand | P47110 |
Ligands and binding sites
- SF4 · Iron/sulfur cluster · ligand · chains A, F
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 | 693 | 0.74 | 0.79 | 84 | empty |
| 2 | 700 | 0.69 | 0.76 | 72 | empty |
| 3 | 388 | 0.69 | 0.81 | 39 | empty |
| 4 | 54 | 0.65 | 0.94 | 18 | empty |
| 5 | 181 | 0.64 | 0.84 | 36 | empty |
Interfaces
7 interfaces between chains.
- F–G · 2803 Ų buried · 37 hydrogen bonds · protein-protein
- A–F · 2532 Ų buried · 22 hydrogen bonds · protein-protein
- A–D · 2288 Ų buried · 21 hydrogen bonds · protein-protein
- A–E · 2177 Ų buried · 26 hydrogen bonds · protein-protein
- D–E · 723 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 7LXD · Structure of yeast 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 0.93
- 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 0.89
- 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 0.84
- 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 0.75
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 7LXD · PDBe 7LXD · UniProt P14284 · UniProt P38927 · UniProt P46957 · UniProt P47110
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