MolNFT v1 · #90241 · protein
The structure of the S. aureus dnag RNA polymerase domain bound to GTP and manganese
4EDK · DNA primase: “The structure of the S. aureus dnag RNA polymerase domain bound to GTP and manganese”. X-ray diffraction, 3 ligands (BEN, GTP, MN), 3 pockets (best druggability 0.46). MolNFT v1 #90241 on GenesisL1: 3D structure…
- PDB
- 4EDK
- Type
- protein
- Length
- 321 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA primase
- EC
- 2.7.7.-
- UniProt
- O05338
- Ligands
- BEN, GTP, MN
- Pockets
- 3 · best druggability 0.46
Structure
x-ray diffraction · 1 distinct chain · 53% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA primase (EC 2.7.7.-) | protein | 321 | 53% helix, 15% strand | O05338 |
Ligands and binding sites
- BEN · Benzamidine · ligand · 3 copies · chains A
- GTP · Guanosine-5'-triphosphate · ligand · chains A
- MN · Manganese (II) ion · metal · 3 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 52 | 0.46 | 0.85 | 13 | empty |
| 2 | 147 | 0.45 | 0.76 | 26 | GTP, MN |
| 3 | 99 | 0.41 | 0.77 | 19 | empty |
Compared structures
- 4EDK · The structure of the S. aureus DnaG RNA Polymerase Domain bound to GTP and Manganese · the same entry in another collection · chain A against A, TM-score 1.00
- O05338 · AlphaFold monomer V2.0 prediction for DNA primase (O05338) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 O05338
- Elsewhere: RCSB PDB 4EDK · PDBe 4EDK · UniProt O05338
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