MolNFT v1 · #70074 · protein
Crystal structure of human polymerase alpha-primase P58 iron-sulfur cluster domain
3L9Q · DNA primase large subunit: “Crystal structure of human polymerase alpha-primase P58 iron-sulfur cluster domain”. X-ray diffraction, 2 ligands (SF4, SO4), 6 pockets (best druggability 0.69). MolNFT v1 #70074 on GenesisL1: 3D…
- PDB
- 3L9Q
- Type
- protein
- Length
- 338 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA primase large subunit
- EC
- 2.7.7.-
- UniProt
- P49643
- Ligands
- SF4, SO4
- Pockets
- 6 · best druggability 0.69
Structure
x-ray diffraction · 2 distinct chains · 56% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA primase large subunit (EC 2.7.7.-) | protein | 171 | 56% helix, 9% strand | P49643 |
| B | DNA primase large subunit (EC 2.7.7.-) | protein | 167 | 56% helix, 6% strand | P49643 |
Ligands and binding sites
- SF4 · Iron/sulfur cluster · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 5 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 446 | 0.69 | 0.80 | 50 | empty |
| 2 | 152 | 0.48 | 0.77 | 24 | empty |
| 3 | 148 | 0.46 | 0.77 | 25 | empty |
| 4 | 110 | 0.40 | 0.76 | 15 | empty |
| 5 | 86 | 0.34 | 0.74 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 869 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 3L9Q · Crystal structure of human polymerase alpha-primase p58 iron-sulfur cluster domain · the same entry in another collection · chain A against A, TM-score 1.00
- P49643 · AlphaFold monomer V2.0 prediction for DNA primase large subunit (P49643) · a predicted model of the same protein · chain B against A, TM-score 0.88
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 P49643
- Elsewhere: RCSB PDB 3L9Q · PDBe 3L9Q · UniProt P49643
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