Research workbench
The structure of the S. aureus dnag RNA polymerase domain bound to pppgpp and manganese
Analyse The structure of the S. aureus dnag RNA polymerase domain bound to pppgpp and… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4EDV
- 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, 0O2, MN
- Pockets
- 2 · best druggability 0.46
Structure
x-ray diffraction · 1 distinct chain · 53% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA primase (EC 2.7.7.-) | protein | 321 | 53% helix, 14% strand | O05338 |
Ligands and binding sites
- BEN · Benzamidine · ligand · chains A
- 0O2 · guanosine 5'-(tetrahydrogen triphosphate) 3'-(trihydrogen diphosphate) · 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
2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 172 | 0.46 | 0.75 | 26 | MN |
| 2 | 85 | 0.41 | 0.78 | 18 | empty |
Compared structures
- 4EDV · The structure of the S. aureus DnaG RNA Polymerase Domain bound to pppGpp 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 4EDV · PDBe 4EDV · UniProt O05338
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