MolNFT v1 · #24159 · protein
Branched-chain 2-oxo acid dehydrogenase (E1) from thermus thermophilus HB8 in apo-form
1UM9 · 2-oxo acid dehydrogenase alpha subunit: “Branched-chain 2-oxo acid dehydrogenase (E1) from thermus thermophilus HB8 in apo-form”. X-ray diffraction, 1 ligand (SO4), 9 pockets (best druggability 0.75). MolNFT v1 #24159 on GenesisL1…
- PDB
- 1UM9
- Type
- protein
- Length
- 1,312 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
- SO4
- Pockets
- 9 · best druggability 0.75
Structure
x-ray diffraction · 3 distinct chains · 45% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 2-oxo acid dehydrogenase alpha subunit (EC 1.2.4.4) | protein | 331 | 47% helix, 11% strand | P84129 |
| B, D | 2-oxo acid dehydrogenase beta subunit (EC 1.2.4.4) | protein | 323 | 42% helix, 20% strand | P84130 |
| C | 2-oxo acid dehydrogenase alpha subunit (EC 1.2.4.4) | protein | 335 | 46% helix, 12% strand | P84129 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 2 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 73 | 0.75 | 0.99 | 20 | empty |
| 2 | 60 | 0.73 | 0.99 | 18 | empty |
| 3 | 615 | 0.69 | 0.78 | 69 | SO4 |
| 4 | 432 | 0.64 | 0.78 | 57 | SO4 |
| 5 | 145 | 0.62 | 0.85 | 28 | empty |
Interfaces
6 interfaces between chains.
- B–D · 2159 Ų buried · 30 hydrogen bonds · protein-protein
- C–D · 1854 Ų buried · 24 hydrogen bonds · protein-protein
- A–B · 1845 Ų buried · 22 hydrogen bonds · protein-protein
- A–D · 1295 Ų buried · 13 hydrogen bonds · protein-protein
- B–C · 1276 Ų buried · 14 hydrogen bonds · protein-protein
Compared structures
- 1UM9 · branched-chain 2-oxo acid dehydrogenase (E1) from Thermus thermophilus HB8 in apo-form · 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 1UM9 · PDBe 1UM9 · UniProt P84129 · UniProt P84130
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.