Research workbench
Crystal structure of B. subtilis purr bound to ppgpp
Analyse Crystal structure of B. subtilis purr bound to ppgpp in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7RMW
- Type
- protein
- Length
- 1,581 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pur operon repressor
- UniProt
- A0A063X7Y1
- Ligands
- G4P
- Pockets
- 15 · best druggability 0.84
Structure
x-ray diffraction · 6 distinct chains · 39% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Pur operon repressor | protein | 270 | 39% helix, 29% strand | A0A063X7Y1 |
| B | Pur operon repressor | protein | 269 | 38% helix, 28% strand | A0A063X7Y1 |
| C | Pur operon repressor | protein | 256 | 39% helix, 29% strand | A0A063X7Y1 |
| D | Pur operon repressor | protein | 261 | 39% helix, 28% strand | A0A063X7Y1 |
| E | Pur operon repressor | protein | 260 | 39% helix, 26% strand | A0A063X7Y1 |
| F | Pur operon repressor | protein | 265 | 39% helix, 29% strand | A0A063X7Y1 |
Ligands and binding sites
- G4P · Guanosine-5',3'-tetraphosphate · ligand · 4 copies · chains A, B, C, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1142 | 0.84 | 0.85 | 137 | G4P |
| 2 | 748 | 0.83 | 0.86 | 62 | empty |
| 3 | 709 | 0.82 | 0.86 | 63 | empty |
| 4 | 732 | 0.82 | 0.86 | 94 | G4P |
| 5 | 708 | 0.80 | 0.84 | 66 | empty |
Interfaces
12 interfaces between chains.
- A–B · 1995 Ų buried · 15 hydrogen bonds · protein-protein
- E–F · 1906 Ų buried · 13 hydrogen bonds · protein-protein
- C–D · 1831 Ų buried · 11 hydrogen bonds · protein-protein
- D–E · 395 Ų buried · 4 hydrogen bonds · protein-protein
- B–D · 254 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 8 covalent (covalent ligand).
Compared structures
- 7RMW · Crystal structure of B. subtilis PurR bound to ppGpp · the same entry in another collection · chain A against A, TM-score 1.00
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 A0A063X7Y1
- Elsewhere: RCSB PDB 7RMW · PDBe 7RMW · UniProt A0A063X7Y1
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