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
- 2BEU
- Type
- protein
- Length
- 728 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 2-oxoisovalerate dehydrogenase alpha subunit; 2-oxoisovalerate dehydrogenase beta…
- EC
- 1.2.4.4
- UniProt
- P12694, P21953
- Ligands
- THV, K, MN, CL, SO4
- Pockets
- 6 · best druggability 0.53
Structure
x-ray diffraction · 3 distinct chains · 42% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 2-oxoisovalerate dehydrogenase alpha subunit (EC 1.2.4.4) | protein | 390 | 47% helix, 10% strand | P12694 |
| B | 2-oxoisovalerate dehydrogenase beta subunit (EC 1.2.4.4) | protein | 335 | 38% helix, 19% strand | P21953 |
| C | Peptide ala-tyr-arg | protein | 3 | 0% helix, 0% strand | — |
Ligands and binding sites
- THV · C2-1-hydroxy-3-methyl-propyl-thiamin diphosphate · ligand · chains A
- K · Potassium ion · metal · 2 copies · chains A, B
- MN · Manganese (II) ion · metal · chains A
- CL · Chloride ion · ion · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · chains A
- GOL · Glycerol · additive · 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, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 245 | 0.53 | 0.76 | 34 | GOL |
| 2 | 98 | 0.46 | 0.80 | 25 | THV, MN |
| 3 | 97 | 0.44 | 0.79 | 22 | empty |
| 4 | 109 | 0.44 | 0.78 | 18 | empty |
| 5 | 64 | 0.31 | 0.75 | 12 | empty |
Interfaces
2 interfaces between chains.
- A–B · 1844 Ų buried · 25 hydrogen bonds · protein-protein
- A–C · 174 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 2BEU · 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 2BEU · PDBe 2BEU · UniProt P12694 · UniProt P21953
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