Research workbench
Crystal structure of pseudomonas putida 2-oxoisovalerate dehydrogenase (branched-chain alpha-keto acid dehydrogenase, E1B)
Analyse Crystal structure of pseudomonas putida 2-oxoisovalerate dehydrogenase… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1QS0
- Type
- protein
- Length
- 745 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
- UniProt
- P09060, P09061
- Ligands
- TPP, COI, MG
- Pockets
- 6 · best druggability 0.59
Structure
x-ray diffraction · 2 distinct chains · 40% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 2-oxoisovalerate dehydrogenase alpha-subunit | protein | 407 | 43% helix, 9% strand | P09060 |
| B | 2-oxoisovalerate dehydrogenase beta-subunit | protein | 338 | 36% helix, 17% strand | P09061 |
Ligands and binding sites
- TPP · Thiamine diphosphate · ligand · chains A
- COI · 2-oxo-4-methylpentanoic acid · ligand · chains B
- MG · Magnesium ion · metal · chains A
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 | 96 | 0.59 | 0.87 | 29 | MG, TPP |
| 2 | 223 | 0.50 | 0.75 | 40 | empty |
| 3 | 96 | 0.42 | 0.78 | 21 | empty |
| 4 | 99 | 0.39 | 0.76 | 24 | empty |
| 5 | 52 | 0.38 | 0.81 | 27 | empty |
Interfaces
1 interface between chains.
- A–B · 1903 Ų buried · 27 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 22 modified, 1 covalent (engineered, covalent ligand).
Compared structures
- 1QS0 · Crystal Structure of Pseudomonas Putida 2-oxoisovalerate Dehydrogenase (Branched-Chain… · the same entry in another collection · chain A against A, TM-score 1.00
- P09061 · AlphaFold monomer V2.0 prediction for 2-oxoisovalerate dehydrogenase subunit beta (P09061) · a predicted model of the same protein · chain B against A, TM-score 1.00
- P09060 · AlphaFold monomer V2.0 prediction for 2-oxoisovalerate dehydrogenase subunit alpha… · a predicted model of the same protein · chain A against A, TM-score 0.99
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 P09060
- Every structure of UniProt P09061
- Elsewhere: RCSB PDB 1QS0 · PDBe 1QS0 · UniProt P09060 · UniProt P09061
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