Research workbench
Crystal structure of the PriS_PriL-Rpa2WH ternary complex from P. abyssi
Analyse Crystal structure of the PriS_PriL-Rpa2WH ternary complex from P. abyssi in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 9F26
- Type
- protein
- Length
- 637 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 3.501
- Source
- Pyrococcus abyssi
- Molecule
- DNA primase small subunit PriS; DNA primase large subunit PriL; RPA32 subunit of the…
- EC
- 2.7.7.-
- UniProt
- Q9V292, Q9V291, Q9V1Z1
- Ligands
- ZN
- Pockets
- 4 · best druggability 0.76
Structure
x-ray diffraction · resolution 3.501 · 3 distinct chains · 55% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA primase small subunit PriS (EC 2.7.7.-) | protein | 346 | 49% helix, 15% strand | Q9V292 |
| B | DNA primase large subunit PriL | protein | 211 | 66% helix, 6% strand | Q9V291 |
| C | RPA32 subunit of the hetero-oligomeric complex involved in homologous recombination | protein | 80 | 53% helix, 10% strand | Q9V1Z1 |
Ligands and binding sites
- ZN · Zinc ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 427 | 0.76 | 0.85 | 48 | empty |
| 2 | 224 | 0.61 | 0.81 | 27 | empty |
| 3 | 180 | 0.51 | 0.78 | 27 | empty |
| 4 | 114 | 0.39 | 0.75 | 19 | empty |
Interfaces
2 interfaces between chains.
- A–B · 1006 Ų buried · 14 hydrogen bonds · protein-protein
- A–C · 975 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- Q9V292 · AlphaFold monomer V2.0 prediction for DNA primase small subunit pris (Q9V292) · a predicted model of the same protein · chain A against A, TM-score 0.99
- Q9V291 · AlphaFold monomer V2.0 prediction for DNA primase large subunit pril (Q9V291) · a predicted model of the same protein · chain B against A, TM-score 0.99
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 Q9V292
- Every structure of UniProt Q9V291
- Every structure of UniProt Q9V1Z1
- Elsewhere: RCSB PDB 9F26 · PDBe 9F26 · UniProt Q9V292 · UniProt Q9V291 · UniProt Q9V1Z1
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