Research workbench
Bacillus subtilis yabj
Analyse Bacillus subtilis yabj in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1QD9
- Type
- protein
- Length
- 372 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Purine regulatory protein yabj
- UniProt
- P37552
- Ligands
- EMC, HG
- Pockets
- 5 · best druggability 0.79
Structure
x-ray diffraction · 1 distinct chain · 31% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Purine regulatory protein yabj | protein | 124 | 31% helix, 31% strand | P37552 |
Ligands and binding sites
- EMC · Ethyl mercury ion · ligand · 2 copies · chains B, C
- HG · Mercury (II) ion · metal · chains A
- ACY · Acetic acid · additive · 6 copies · chains A, C, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 109 | 0.79 | 0.98 | 27 | empty |
| 2 | 140 | 0.62 | 0.85 | 21 | empty |
| 3 | 178 | 0.61 | 0.83 | 22 | empty |
| 4 | 152 | 0.59 | 0.83 | 21 | empty |
| 5 | 88 | 0.56 | 0.86 | 15 | empty |
Interfaces
3 interfaces between chains.
- B–C · 969 Ų buried · 18 hydrogen bonds · protein-protein
- A–C · 962 Ų buried · 18 hydrogen bonds · protein-protein
- A–B · 940 Ų buried · 16 hydrogen bonds · protein-protein
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 P37552
- Elsewhere: RCSB PDB 1QD9 · PDBe 1QD9 · UniProt P37552
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