Research workbench
Reactivity modulation of human branched-chain alpha-ketoacid dehydrogenase by an internal molecular switch
Analyse Reactivity modulation of human branched-chain alpha-ketoacid dehydrogenase by… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2BFE
- Type
- protein
- Length
- 704 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 2-oxoisovalerate dehydrogenase alpha subunit; 2-oxoisovalerate dehydrogenase beta subunit
- EC
- 1.2.4.4
- UniProt
- P12694, P21953
- Ligands
- TPP, K, MN, CL
- Pockets
- 7 · best druggability 0.61
Structure
x-ray diffraction · 2 distinct chains · 44% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 2-oxoisovalerate dehydrogenase alpha subunit (EC 1.2.4.4) | protein | 375 | 46% helix, 10% strand | P12694 |
| B | 2-oxoisovalerate dehydrogenase beta subunit (EC 1.2.4.4) | protein | 329 | 42% helix, 20% strand | P21953 |
Ligands and binding sites
- TPP · Thiamine diphosphate · ligand · chains A
- K · Potassium ion · metal · 2 copies · chains A, B
- MN · Manganese (II) ion · metal · chains A
- CL · Chloride ion · ion · chains A
- GOL · Glycerol · additive · chains A, B
- MRD · (4R)-2-methylpentane-2,4-diol · additive · chains 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 184 | 0.61 | 0.83 | 28 | CL, TPP |
| 2 | 290 | 0.55 | 0.76 | 37 | GOL |
| 3 | 101 | 0.46 | 0.79 | 20 | empty |
| 4 | 85 | 0.39 | 0.78 | 14 | empty |
| 5 | 76 | 0.33 | 0.74 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 1817 Ų buried · 22 hydrogen bonds · protein-protein
Compared structures
- 2BFE · Reactivity modulation of human branched-chain alpha-ketoacid dehydrogenase by an internal… · the same entry in another collection · chain A against A, TM-score 1.00
- P21953 · AlphaFold monomer V2.0 prediction for 2-oxoisovalerate dehydrogenase subunit beta… · a predicted model of the same protein · chain B against A, TM-score 1.00
- P12694 · AlphaFold monomer V2.0 prediction for 2-oxoisovalerate dehydrogenase subunit alpha… · a predicted model of the same protein · 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 P12694
- Every structure of UniProt P21953
- Elsewhere: RCSB PDB 2BFE · PDBe 2BFE · UniProt P12694 · UniProt P21953
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