MolNFT v1 · #107137 · protein
Crystal structure of yvoa from bacillus subtilis in complex with glucosamine-6-phosphate
4U0V · Hth-type transcriptional repressor yvoa: “Crystal structure of yvoa from bacillus subtilis in complex with glucosamine-6-phosphate”. X-ray diffraction, 1 ligand (GLP), 6 pockets (best druggability 0.75). MolNFT v1 #107137 on…
- PDB
- 4U0V
- Type
- protein
- Length
- 485 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hth-type transcriptional repressor yvoa
- UniProt
- O34817
- Ligands
- GLP
- Pockets
- 6 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 31% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hth-type transcriptional repressor yvoa | protein | 243 | 31% helix, 36% strand | O34817 |
| B | Hth-type transcriptional repressor yvoa | protein | 242 | 31% helix, 37% strand | O34817 |
Ligands and binding sites
- GLP · 2-amino-2-deoxy-6-O-phosphono-alpha-D-glucopyranose · ligand · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 24 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 98 | 0.75 | 0.96 | 28 | GLP, EDO |
| 2 | 73 | 0.73 | 0.98 | 24 | GLP |
| 3 | 339 | 0.57 | 0.76 | 34 | EDO |
| 4 | 327 | 0.56 | 0.76 | 33 | empty |
| 5 | 60 | 0.27 | 0.73 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 1644 Ų buried · 35 hydrogen bonds · protein-protein
Compared structures
- 4U0V · Crystal structure of YvoA from Bacillus subtilis in complex with glucosamine-6-phosphate · 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 4U0V · PDBe 4U0V · UniProt O34817
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