MolNFT v1 · #24632 · protein
Crosstalk between cofactor binding and the phosphorylation loop conformation in the bckd machine
1V16 · 2-oxoisovalerate dehydrogenase alpha subunit: “Crosstalk between cofactor binding and the phosphorylation loop conformation in the bckd machine”. X-ray diffraction, 5 ligands (TPP, BEN, K), 6 pockets (best druggability 0.54). MolNFT…
- PDB
- 1V16
- Type
- protein
- Length
- 707 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
- 6 · 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 | 371 | 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 · 4 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
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 255 | 0.54 | 0.76 | 35 | GOL |
| 2 | 151 | 0.52 | 0.80 | 25 | MN, TPP |
| 3 | 96 | 0.44 | 0.79 | 18 | empty |
| 4 | 96 | 0.39 | 0.77 | 15 | empty |
| 5 | 86 | 0.34 | 0.74 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 1852 Ų buried · 26 hydrogen bonds · protein-protein
Compared structures
- 1V16 · 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 1V16 · PDBe 1V16 · UniProt P12694 · UniProt P21953
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