Research workbench
Biotin carboxylase domain of thermophilic 2-oxoglutarate carboxylase bound to bicarbonate
Analyse Biotin carboxylase domain of thermophilic 2-oxoglutarate carboxylase bound to… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7KBL
- Type
- protein
- Length
- 894 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 2-oxoglutarate carboxylase small subunit
- EC
- 6.4.1.7
- UniProt
- D3DJ42
- Ligands
- BCT
- Pockets
- 7 · best druggability 0.70
Structure
x-ray diffraction · 2 distinct chains · 36% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 2-oxoglutarate carboxylase small subunit (EC 6.4.1.7) | protein | 443 | 37% helix, 25% strand | D3DJ42 |
| B | 2-oxoglutarate carboxylase small subunit (EC 6.4.1.7) | protein | 451 | 36% helix, 25% strand | D3DJ42 |
Ligands and binding sites
- BCT · Bicarbonate ion · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 499 | 0.70 | 0.80 | 54 | empty |
| 2 | 468 | 0.68 | 0.79 | 78 | BCT |
| 3 | 363 | 0.59 | 0.76 | 54 | BCT |
| 4 | 257 | 0.50 | 0.74 | 39 | empty |
| 5 | 87 | 0.48 | 0.82 | 25 | empty |
Interfaces
1 interface between chains.
- A–B · 1588 Ų buried · 32 hydrogen bonds · protein-protein
Compared structures
- 7KBL · Biotin Carboxylase domain of Thermophilic 2-Oxoglutarate Carboxylase bound to Bicarbonate · the same entry in another collection · chain B against B, TM-score 1.00
- D3DJ42 · AlphaFold monomer V2.0 prediction for 2-oxoglutarate carboxylase small subunit (D3DJ42) · a predicted model of the same protein · chain A against A, TM-score 0.97
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 D3DJ42
- Elsewhere: RCSB PDB 7KBL · PDBe 7KBL · UniProt D3DJ42
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