Research workbench
Crystal structure of yvoa from bacillus subtilis in complex with N- acetylglucosamine-6-phosphate
Analyse Crystal structure of yvoa from bacillus subtilis in complex with N… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4U0W
- Type
- protein
- Length
- 486 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hth-type transcriptional repressor yvoa
- UniProt
- O34817
- Ligands
- 16G
- Pockets
- 5 · best druggability 0.76
Structure
x-ray diffraction · 1 distinct chain · 31% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Hth-type transcriptional repressor yvoa | protein | 243 | 31% helix, 36% strand | O34817 |
Ligands and binding sites
- 16G · 2-acetamido-2-deoxy-6-O-phosphono-alpha-D-glucopyranose · ligand · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 13 copies · chains A, B
- GOL · Glycerol · additive · 2 copies · chains A, 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, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 103 | 0.76 | 0.97 | 28 | 16G |
| 2 | 98 | 0.75 | 0.96 | 26 | 16G |
| 3 | 348 | 0.58 | 0.76 | 36 | EDO |
| 4 | 289 | 0.55 | 0.76 | 30 | EDO |
| 5 | 105 | 0.37 | 0.74 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 1719 Ų buried · 37 hydrogen bonds · protein-protein
Compared structures
- 4U0W · Crystal structure of YvoA from Bacillus subtilis in complex with… · the same entry in another collection · chain A against A, TM-score 1.00
- O34817 · AlphaFold monomer V2.0 prediction for hth-type transcriptional repressor nagr (O34817) · a predicted model of the same protein · chain A against A, TM-score 0.72
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 O34817
- Elsewhere: RCSB PDB 4U0W · PDBe 4U0W · UniProt O34817
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