MolNFT v1 · #190105 · protein
Cryo-electron microscopic structure of the 2-oxoglutarate dehydrogenase (E1) component of the human alpha-ketoglutarate (2- oxoglutarate) dehydrogenase complex
7WGR · 2-oxoglutarate dehydrogenase, mitochondrial: “Cryo-electron microscopic structure of the 2-oxoglutarate dehydrogenase (E1) component of the human…”. Electron microscopy, 3 ligands (TPP, CA, MG), 20 pockets (best druggability 0.90).…
- PDB
- 7WGR
- Type
- protein
- Length
- 1,700 residues
- Chains
- 2
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 2-oxoglutarate dehydrogenase, mitochondrial
- EC
- 1.2.4.2
- UniProt
- Q02218
- Ligands
- TPP, CA, MG
- Pockets
- 20 · best druggability 0.90
Structure
electron microscopy · 1 distinct chain · 41% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | 2-oxoglutarate dehydrogenase, mitochondrial (EC 1.2.4.2) | protein | 850 | 41% helix, 13% strand | Q02218 |
Ligands and binding sites
- TPP · Thiamine diphosphate · ligand · 2 copies · chains A, B
- CA · Calcium ion · metal · 2 copies · chains A, B
- 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
20 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 809 | 0.90 | 0.94 | 137 | MG, TPP |
| 2 | 1153 | 0.83 | 0.84 | 117 | empty |
| 3 | 599 | 0.78 | 0.84 | 68 | empty |
| 4 | 54 | 0.71 | 0.99 | 21 | empty |
| 5 | 109 | 0.71 | 0.93 | 26 | empty |
Interfaces
1 interface between chains.
- A–B · 5070 Ų buried · 44 hydrogen bonds · protein-protein
Compared structures
- 7WGR · Cryo-electron microscopic structure of the 2-oxoglutarate dehydrogenase (E1) component of… · the same entry in another collection · chain A against A, TM-score 1.00
- Q02218 · AlphaFold monomer V2.0 prediction for 2-oxoglutarate dehydrogenase, mitochondrial (Q02218) · a predicted model of the same protein · chain A against A, TM-score 0.98
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 Q02218
- Elsewhere: RCSB PDB 7WGR · PDBe 7WGR · UniProt Q02218
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