Research workbench
Crosstalk between cofactor binding and the phosphorylation loop conformation in the bckd machine
Analyse Crosstalk between cofactor binding and the phosphorylation loop conformation in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1V11
- Type
- protein
- Length
- 706 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, BEN, K, MN, CL
- Pockets
- 8 · best druggability 0.54
Structure
x-ray diffraction · 2 distinct chains · 43% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 2-oxoisovalerate dehydrogenase alpha subunit (EC 1.2.4.4) | protein | 370 | 47% helix, 11% strand | P12694 |
| B | 2-oxoisovalerate dehydrogenase beta subunit (EC 1.2.4.4) | protein | 336 | 40% helix, 19% strand | P21953 |
Ligands and binding sites
- TPP · Thiamine diphosphate · ligand · chains A
- BEN · Benzamidine · ligand · chains A
- K · Potassium ion · metal · 2 copies · chains A, B
- MN · Manganese (II) ion · metal · chains A
- CL · Chloride ion · ion · 5 copies · chains B, A
- GOL · Glycerol · additive · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 259 | 0.54 | 0.76 | 32 | GOL |
| 2 | 104 | 0.45 | 0.79 | 19 | MN, TPP |
| 3 | 99 | 0.45 | 0.79 | 20 | empty |
| 4 | 73 | 0.35 | 0.77 | 13 | empty |
| 5 | 82 | 0.33 | 0.74 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 1849 Ų buried · 23 hydrogen bonds · protein-protein
Compared structures
- 1V11 · Crosstalk between cofactor binding and the phosphorylation loop conformation in the bckd… · 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 1V11 · PDBe 1V11 · UniProt P12694 · UniProt P21953
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