MolNFT v1 · #146449 · protein
Crystal structure of primase iron-sulfur domain (266-457)
6DHW · DNA primase large subunit: “Crystal structure of primase iron-sulfur domain (266-457)”. X-ray diffraction, 2 ligands (SF4, SO4), 6 pockets (best druggability 0.67). MolNFT v1 #146449 on GenesisL1: 3D structure, binding sites and…
- PDB
- 6DHW
- Type
- protein
- Length
- 336 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 0.67
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 | 170 | 56% helix, 9% strand | P49643 |
| B | DNA primase large subunit (EC 2.7.7.-) | protein | 166 | 57% helix, 6% strand | P49643 |
Ligands and binding sites
- SF4 · Iron/sulfur cluster · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 6 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 381 | 0.67 | 0.80 | 37 | SO4 |
| 2 | 194 | 0.51 | 0.77 | 34 | SO4 |
| 3 | 108 | 0.43 | 0.78 | 23 | empty |
| 4 | 102 | 0.37 | 0.75 | 15 | empty |
| 5 | 75 | 0.32 | 0.74 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 911 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
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 6DHW · PDBe 6DHW · UniProt P49643
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