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Branched-chain 2-oxo acid dehydrogenase (E1) from thermus thermophilus HB8 with 4-methylpentanoate
Analyse Branched-chain 2-oxo acid dehydrogenase (E1) from thermus thermophilus HB8 with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1UMC
- Type
- protein
- Length
- 1,369 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 2-oxo acid dehydrogenase alpha subunit; 2-oxo acid dehydrogenase beta subunit
- EC
- 1.2.4.4
- UniProt
- P84129, P84130
- Ligands
- TPP, 4MV, MG
- Pockets
- 13 · best druggability 0.84
Structure
x-ray diffraction · 3 distinct chains · 44% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 2-oxo acid dehydrogenase alpha subunit (EC 1.2.4.4) | protein | 362 | 46% helix, 11% strand | P84129 |
| B, D | 2-oxo acid dehydrogenase beta subunit (EC 1.2.4.4) | protein | 323 | 41% helix, 20% strand | P84130 |
| C | 2-oxo acid dehydrogenase alpha subunit (EC 1.2.4.4) | protein | 361 | 47% helix, 11% strand | P84129 |
Ligands and binding sites
- TPP · Thiamine diphosphate · ligand · 2 copies · chains A, D, B, C
- 4MV · 4-methyl valeric acid · ligand · chains A, D
- MG · Magnesium ion · metal · 2 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 261 | 0.84 | 0.95 | 49 | MG, TPP, 4MV |
| 2 | 178 | 0.82 | 0.96 | 31 | empty |
| 3 | 445 | 0.77 | 0.85 | 59 | MG, TPP |
| 4 | 56 | 0.72 | 0.99 | 20 | empty |
| 5 | 165 | 0.64 | 0.85 | 30 | empty |
Interfaces
6 interfaces between chains.
- B–D · 2063 Ų buried · 29 hydrogen bonds · protein-protein
- C–D · 1874 Ų buried · 22 hydrogen bonds · protein-protein
- A–B · 1844 Ų buried · 21 hydrogen bonds · protein-protein
- A–D · 1618 Ų buried · 20 hydrogen bonds · protein-protein
- B–C · 1600 Ų buried · 18 hydrogen bonds · protein-protein
Compared structures
- 1UMC · branched-chain 2-oxo acid dehydrogenase (E1) from Thermus thermophilus HB8 with… · the same entry in another collection · 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 P84129
- Every structure of UniProt P84130
- Elsewhere: RCSB PDB 1UMC · PDBe 1UMC · UniProt P84129 · UniProt P84130
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