Research workbench
2-amino-3-ketobutyrate CoA ligase from cupriavidus necator glycine binding form
Analyse 2-amino-3-ketobutyrate CoA ligase from cupriavidus necator glycine binding form in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7BXS
- Type
- protein
- Length
- 798 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 2-amino-3-ketobutyrate coenzyme a ligase
- EC
- 2.3.1.29
- UniProt
- Q0K313
- Ligands
- PLG
- Pockets
- 9 · best druggability 0.86
Structure
x-ray diffraction · 1 distinct chain · 45% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | 2-amino-3-ketobutyrate coenzyme a ligase (EC 2.3.1.29) | protein | 399 | 45% helix, 17% strand | Q0K313 |
Ligands and binding sites
- PLG · N-glycine-[3-hydroxy-2-methyl-5-phosphonooxymethyl-pyridin-4-yl-methane] · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 290 | 0.86 | 0.97 | 74 | PLG |
| 2 | 55 | 0.71 | 0.98 | 22 | empty |
| 3 | 266 | 0.54 | 0.76 | 38 | empty |
| 4 | 275 | 0.53 | 0.75 | 35 | empty |
| 5 | 59 | 0.48 | 0.85 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 4820 Ų buried · 85 hydrogen bonds · protein-protein
Compared structures
- 7BXS · 2-amino-3-ketobutyrate CoA ligase from Cupriavidus necator glycine binding form · the same entry in another collection · chain A against A, TM-score 1.00
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 Q0K313
- Elsewhere: RCSB PDB 7BXS · PDBe 7BXS · UniProt Q0K313
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