Research workbench
Crystal structure of the heterotrimeric prislx primase from S. solfataricus.
Analyse Crystal structure of the heterotrimeric prislx primase from S. solfataricus. in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5OFN
- Type
- protein
- Length
- 624 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA primase small subunit pris; DNA primase large subunit PRIL,PRIL-X fusion protein
- EC
- 2.7.7.-
- UniProt
- Q97Z83, Q9UWW1
- Ligands
- ZN
- Pockets
- 7 · best druggability 0.73
Structure
x-ray diffraction · 3 distinct chains · 44% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA primase small subunit pris (EC 2.7.7.-) | protein | 319 | 28% helix, 26% strand | Q97Z83 |
| B | DNA primase large subunit PRIL,PRIL-X fusion protein | protein | 206 | 58% helix, 12% strand | Q9UWW1 |
| C | DNA primase large subunit PRIL,PRIL-X fusion protein | protein | 99 | 66% helix, 0% strand | Q9UWW1 |
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
7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 945 | 0.73 | 0.77 | 85 | empty |
| 2 | 198 | 0.57 | 0.80 | 29 | empty |
| 3 | 129 | 0.47 | 0.77 | 16 | empty |
| 4 | 110 | 0.39 | 0.75 | 26 | empty |
| 5 | 121 | 0.37 | 0.73 | 23 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1040 Ų buried · 4 hydrogen bonds · protein-protein
- B–C · 341 Ų buried · 6 hydrogen bonds · protein-protein
- A–C · 155 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 5OFN · Crystal structure of the heterotrimeric PriSLX primase from S. solfataricus. · the same entry in another collection · chain A against A, TM-score 1.00
- Q9UWW1 · AlphaFold monomer V2.0 prediction for DNA primase large subunit pril (Q9UWW1) · a predicted model of the same protein · chain B against A, TM-score 0.98
- Q97Z83 · AlphaFold monomer V2.0 prediction for DNA primase small subunit pris (Q97Z83) · a predicted model of the same protein · chain A against A, TM-score 0.98
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 Q97Z83
- Every structure of UniProt Q9UWW1
- Elsewhere: RCSB PDB 5OFN · PDBe 5OFN · UniProt Q97Z83 · UniProt Q9UWW1
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