Research workbench
Crystal structure of the hydrogenobacter thermophilus 2-oxoglutarate carboxylase (ogc) biotin carboxylase (bc) domain dimer in complex with adenosine 5'-diphosphate magnesium salt (mgadp), adenosine 5'- diphosphate (ADP, and bicarbonate anion (hydrogen CARBONATE/HCO3-)
Analyse Crystal structure of the hydrogenobacter thermophilus 2-oxoglutarate… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7KCT
- Type
- protein
- Length
- 906 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, BCT, MG
- Pockets
- 6 · best druggability 0.80
Structure
x-ray diffraction · 1 distinct chain · 37% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | 2-oxoglutarate carboxylase small subunit (EC 6.4.1.7) | protein | 453 | 37% helix, 24% strand | D3DJ42 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 4 copies · chains A, B
- BCT · Bicarbonate ion · ligand · chains A
- MG · Magnesium ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1084 | 0.80 | 0.81 | 129 | ADP, MG |
| 2 | 882 | 0.79 | 0.81 | 87 | ADP, MG |
| 3 | 462 | 0.72 | 0.82 | 40 | empty |
| 4 | 131 | 0.38 | 0.73 | 21 | empty |
| 5 | 67 | 0.35 | 0.77 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 1561 Ų buried · 31 hydrogen bonds · protein-protein
Compared structures
- 7KCT · Crystal Structure of the Hydrogenobacter thermophilus 2-Oxoglutarate Carboxylase (OGC)… · 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 A against A, TM-score 0.90
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 7KCT · PDBe 7KCT · UniProt D3DJ42
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