Research workbench
Structure of the effector-binding domain of deoxyribonucleoside regulator deor from bacillus subtilis
Analyse Structure of the effector-binding domain of deoxyribonucleoside regulator deor… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4OQQ
- Type
- protein
- Length
- 508 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Deoxyribonucleoside regulator
- UniProt
- P39140
- Ligands
- BCN
- Pockets
- 7 · best druggability 0.85
Structure
x-ray diffraction · 1 distinct chain · 44% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Deoxyribonucleoside regulator | protein | 254 | 44% helix, 17% strand | P39140 |
Ligands and binding sites
- BCN · Bicine · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 285 | 0.85 | 0.96 | 35 | empty |
| 2 | 306 | 0.70 | 0.84 | 34 | BCN |
| 3 | 279 | 0.70 | 0.84 | 32 | BCN |
| 4 | 58 | 0.50 | 0.86 | 17 | empty |
| 5 | 53 | 0.49 | 0.86 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 1462 Ų buried · 18 hydrogen bonds · protein-protein
Compared structures
- 4OQQ · Structure of the effector-binding domain of deoxyribonucleoside regulator DeoR from… · the same entry in another collection · chain A against A, TM-score 1.00
- P39140 · AlphaFold monomer V2.0 prediction for deoxyribonucleoside regulator (P39140) · a predicted model of the same protein · chain B against A, TM-score 0.98
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 P39140
- Elsewhere: RCSB PDB 4OQQ · PDBe 4OQQ · UniProt P39140
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