MolNFT v1 · #116854 · protein
Crystal structure of Y347F mutant of human primase P58 iron-sulfur cluster domain
5DQO · DNA primase large subunit: “Crystal structure of Y347F mutant of human primase P58 iron-sulfur cluster domain”. X-ray diffraction, 1 ligand (SF4), 10 pockets (best druggability 0.72). MolNFT v1 #116854 on GenesisL1: 3D structure…
- PDB
- 5DQO
- Type
- protein
- Length
- 629 residues
- Chains
- 4
- 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
- Pockets
- 10 · best druggability 0.72
Structure
x-ray diffraction · 4 distinct chains · 58% helix, 6% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA primase large subunit (EC 2.7.7.-) | protein | 158 | 61% helix, 6% strand | P49643 |
| B | DNA primase large subunit (EC 2.7.7.-) | protein | 154 | 58% helix, 4% strand | P49643 |
| C | DNA primase large subunit (EC 2.7.7.-) | protein | 158 | 56% helix, 5% strand | P49643 |
| D | DNA primase large subunit (EC 2.7.7.-) | protein | 159 | 56% helix, 7% strand | P49643 |
Ligands and binding sites
- SF4 · Iron/sulfur cluster · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 270 | 0.72 | 0.86 | 47 | empty |
| 2 | 225 | 0.63 | 0.82 | 31 | empty |
| 3 | 163 | 0.47 | 0.76 | 30 | empty |
| 4 | 138 | 0.45 | 0.76 | 21 | empty |
| 5 | 105 | 0.44 | 0.78 | 22 | empty |
Interfaces
4 interfaces between chains.
- C–D · 889 Ų buried · 6 hydrogen bonds · protein-protein
- A–B · 873 Ų buried · 10 hydrogen bonds · protein-protein
- A–D · 353 Ų buried · 2 hydrogen bonds · protein-protein
- B–C · 130 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 5DQO · Crystal structure of Y347F mutant of human primase p58 iron-sulfur cluster domain · the same entry in another collection · chain D against D, 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 0.93
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 5DQO · PDBe 5DQO · UniProt P49643
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