Research workbench
Suicide inhibition of a-oxamine synthase: structures of the covalent adducts of 8-amino-7-oxonanoate synthase with trifluoroalanine
Analyse Suicide inhibition of a-oxamine synthase: structures of the covalent adducts of… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2G6W
- Type
- protein
- Length
- 383 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 8-amino-7-oxononanoate synthase
- EC
- 2.3.1.47
- UniProt
- P12998
- Ligands
- LLF
- Pockets
- 3 · best druggability 0.57
Structure
x-ray diffraction · 1 distinct chain · 44% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 8-amino-7-oxononanoate synthase (EC 2.3.1.47) | protein | 383 | 44% helix, 19% strand | P12998 |
Ligands and binding sites
- LLF · (4-{(E)-[(2,2-difluoroethyl)imino]methyl}-5-hydroxy-6-methylpyridin-3-yl)methyl dihydrogen phosphate · ligand · chains A
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 | 86 | 0.57 | 0.87 | 19 | empty |
| 2 | 205 | 0.44 | 0.73 | 30 | empty |
| 3 | 57 | 0.34 | 0.78 | 17 | LLF |
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 2G6W · Suicide inhibition of a-Oxamine Synthase: Structures of the Covalent Adducts of… · the same entry in another collection · chain A against A, TM-score 1.00
- P12998 · AlphaFold monomer V2.0 prediction for 8-amino-7-oxononanoate synthase (P12998) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 P12998
- Elsewhere: RCSB PDB 2G6W · PDBe 2G6W · UniProt P12998
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