MolNFT v1 · #90248 · protein
The structure of the S. aureus dnag RNA polymerase domain bound to UTP and manganese
4EDR · DNA primase: “The structure of the S. aureus dnag RNA polymerase domain bound to UTP and manganese”. X-ray diffraction, 3 ligands (BEN, UTP, MN), 4 pockets (best druggability 0.45). MolNFT v1 #90248 on GenesisL1: 3D structure…
- PDB
- 4EDR
- 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, UTP, MN
- Pockets
- 4 · best druggability 0.45
Structure
x-ray diffraction · 1 distinct chain · 54% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA primase (EC 2.7.7.-) | protein | 321 | 54% helix, 14% strand | O05338 |
Ligands and binding sites
- BEN · Benzamidine · ligand · 3 copies · chains A
- UTP · Uridine 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
4 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 55 | 0.45 | 0.84 | 14 | empty |
| 2 | 129 | 0.40 | 0.75 | 18 | UTP, MN |
| 3 | 56 | 0.36 | 0.79 | 13 | empty |
| 4 | 82 | 0.36 | 0.76 | 17 | empty |
Compared structures
- 4EDR · The structure of the S. aureus DnaG RNA Polymerase Domain bound to UTP 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 4EDR · PDBe 4EDR · UniProt O05338
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