MolNFT v1 · #48365 · protein
Crystal structure of the bacillus subtilis N-acetyltransferase ylbp protein in complex with coenzyme-a
2PR1 · Uncharacterized N-acetyltransferase ylbp: “Crystal structure of the bacillus subtilis N-acetyltransferase ylbp protein in complex with coenzyme-a”. X-ray diffraction, 5 ligands (COA, GLC, FRU), 3 pockets (best druggability 0.79).…
- PDB
- 2PR1
- Type
- protein
- Length
- 301 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Uncharacterized N-acetyltransferase ylbp
- EC
- 2.3.1.-
- UniProt
- O34468
- Ligands
- COA, GLC, FRU, CO, SO4
- Pockets
- 3 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 31% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Uncharacterized N-acetyltransferase ylbp (EC 2.3.1.-) | protein | 152 | 32% helix, 28% strand | O34468 |
| B | Uncharacterized N-acetyltransferase ylbp (EC 2.3.1.-) | protein | 149 | 30% helix, 26% strand | O34468 |
Ligands and binding sites
- COA · Coenzyme A · ligand · 2 copies · chains A, B
- GLC · alpha-D-glucopyranose · sugar · 2 copies · chains A, B
- FRU · beta-D-fructofuranose · sugar · 2 copies · chains A, B
- CO · Cobalt (II) ion · metal · 2 copies · chains B
- SO4 · Sulfate ion · ion · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 950 | 0.79 | 0.81 | 94 | SO4, COA |
| 2 | 68 | 0.34 | 0.76 | 14 | empty |
| 3 | 69 | 0.32 | 0.75 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 1099 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 2PR1 · Crystal structure of the Bacillus subtilis N-acetyltransferase YlbP protein in complex… · the same entry in another collection · chain A against A, TM-score 1.00
- O34468 · AlphaFold monomer V2.0 prediction for uncharacterized N-acetyltransferase ylbp (O34468) · a predicted model of the same protein · chain A 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 O34468
- Elsewhere: RCSB PDB 2PR1 · PDBe 2PR1 · UniProt O34468
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