MolNFT v1 · #121853 · protein
Crystal structure of Y345F mutant of human primase P58 iron-sulfur cluster domain
5I7M · DNA primase large subunit: “Crystal structure of Y345F mutant of human primase P58 iron-sulfur cluster domain”. X-ray diffraction, 2 ligands (SF4, SO4), 6 pockets (best druggability 0.66). MolNFT v1 #121853 on GenesisL1: 3D…
- PDB
- 5I7M
- Type
- protein
- Length
- 329 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 0.66
Structure
x-ray diffraction · 2 distinct chains · 57% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA primase large subunit (EC 2.7.7.-) | protein | 167 | 57% helix, 10% strand | P49643 |
| B | DNA primase large subunit (EC 2.7.7.-) | protein | 162 | 57% helix, 6% strand | P49643 |
Ligands and binding sites
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 | 383 | 0.66 | 0.80 | 40 | empty |
| 2 | 156 | 0.47 | 0.76 | 31 | empty |
| 3 | 161 | 0.47 | 0.76 | 30 | empty |
| 4 | 67 | 0.31 | 0.74 | 18 | empty |
| 5 | 77 | 0.31 | 0.73 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 786 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 5I7M · Crystal structure of Y345F mutant of human 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 0.89
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 5I7M · PDBe 5I7M · UniProt P49643
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