Research workbench
Crystal structure of the PRI1 subunit of human primase bound to fludarabine triphosphate
Analyse Crystal structure of the PRI1 subunit of human primase bound to fludarabine… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6R4U
- Type
- protein
- Length
- 764 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA primase small subunit
- EC
- 2.7.7.-
- UniProt
- P49642
- Ligands
- HFD, MN, ZN
- Pockets
- 13 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 49% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA primase small subunit (EC 2.7.7.-) | protein | 382 | 48% helix, 12% strand | P49642 |
| E | DNA primase small subunit (EC 2.7.7.-) | protein | 382 | 49% helix, 12% strand | P49642 |
Ligands and binding sites
- HFD · 2-fluoro-9-{5-O-[(R)-hydroxy{[(r)-hydroxy(phosphonooxy)phosphoryl]oxy}phosphoryl]-beta-D-arabinofuranosyl}-9H-purin-6-amine · ligand · 2 copies · chains A, E
- MN · Manganese (II) ion · metal · 4 copies · chains A, E
- ZN · Zinc ion · metal · 2 copies · chains A, E
- EDO · 1,2-ethanediol · additive · chains E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1181 | 0.75 | 0.78 | 95 | empty |
| 2 | 89 | 0.50 | 0.83 | 16 | empty |
| 3 | 172 | 0.48 | 0.77 | 23 | MN, HFD |
| 4 | 97 | 0.47 | 0.81 | 15 | empty |
| 5 | 162 | 0.46 | 0.76 | 22 | MN, HFD |
Interfaces
1 interface between chains.
- A–E · 937 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 6R4U · Crystal structure of the Pri1 subunit of human primase bound to fludarabine triphosphate · the same entry in another collection · chain A against A, TM-score 1.00
- P49642 · AlphaFold monomer V2.0 prediction for DNA primase small subunit (P49642) · a predicted model of the same protein · chain E against A, TM-score 0.97
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 P49642
- Elsewhere: RCSB PDB 6R4U · PDBe 6R4U · UniProt P49642
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