MolNFT v1 · #179655 · protein
Biotin carboxylase domain of thermophilic 2-oxoglutarate carboxylase bound to ADP without magnesium with disordered phosphate tail
7KC7 · 2-oxoglutarate carboxylase small subunit: “Biotin carboxylase domain of thermophilic 2-oxoglutarate carboxylase bound to ADP without magnesium with…”. X-ray diffraction, 2 ligands (ADP, PO4), 9 pockets (best druggability 0.72).…
- PDB
- 7KC7
- Type
- protein
- Length
- 902 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
- ADP, PO4
- Pockets
- 9 · best druggability 0.72
Structure
x-ray diffraction · 1 distinct chain · 37% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | 2-oxoglutarate carboxylase small subunit (EC 6.4.1.7) | protein | 451 | 37% helix, 25% strand | D3DJ42 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · chains A
- PO4 · Phosphate ion · ion · 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 | 451 | 0.72 | 0.82 | 41 | empty |
| 2 | 811 | 0.70 | 0.76 | 76 | PO4, ADP |
| 3 | 143 | 0.55 | 0.82 | 30 | empty |
| 4 | 308 | 0.55 | 0.75 | 47 | PO4 |
| 5 | 99 | 0.46 | 0.80 | 21 | empty |
Interfaces
1 interface between chains.
- A–B · 1563 Ų buried · 32 hydrogen bonds · protein-protein
Compared structures
- 7KC7 · Biotin Carboxylase domain of Thermophilic 2-Oxoglutarate Carboxylase bound to ADP without… · the same entry in another collection · chain A against A, 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 B 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 7KC7 · PDBe 7KC7 · UniProt D3DJ42
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