MolNFT v1 · #24163 · protein
Branched-chain 2-oxo acid dehydrogenase (E1) from thermus thermophilus HB8 with 4-methyl-2-oxopentanoate as an intermediate
1UMD · 2-oxo acid dehydrogenase alpha subunit: “Branched-chain 2-oxo acid dehydrogenase (E1) from thermus thermophilus HB8 with 4-methyl-2-oxopentanoate as…”. X-ray diffraction, 3 ligands (TPP, COI, MG), 12 pockets (best druggability…
- PDB
- 1UMD
- 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
- Q5SLR4, Q5SLR3
- Ligands
- TPP, COI, MG
- Pockets
- 12 · best druggability 0.77
Structure
x-ray diffraction · 3 distinct chains · 45% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 2-oxo acid dehydrogenase alpha subunit (EC 1.2.4.4) | protein | 362 | 47% helix, 10% strand | Q5SLR4 |
| B, D | 2-oxo acid dehydrogenase beta subunit (EC 1.2.4.4) | protein | 323 | 42% helix, 20% strand | Q5SLR3 |
| C | 2-oxo acid dehydrogenase alpha subunit (EC 1.2.4.4) | protein | 361 | 46% helix, 11% strand | Q5SLR4 |
Ligands and binding sites
- TPP · Thiamine diphosphate · ligand · 2 copies · chains A, D, B, C
- COI · 2-oxo-4-methylpentanoic acid · ligand · 2 copies · chains A, D, B, C
- 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
12 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 383 | 0.77 | 0.87 | 55 | MG, TPP, COI |
| 2 | 431 | 0.76 | 0.85 | 60 | MG, TPP, COI |
| 3 | 65 | 0.74 | 0.99 | 20 | empty |
| 4 | 66 | 0.74 | 0.99 | 19 | empty |
| 5 | 160 | 0.59 | 0.83 | 25 | empty |
Interfaces
6 interfaces between chains.
- B–D · 2164 Ų buried · 30 hydrogen bonds · protein-protein
- C–D · 1865 Ų buried · 20 hydrogen bonds · protein-protein
- A–B · 1843 Ų buried · 22 hydrogen bonds · protein-protein
- B–C · 1622 Ų buried · 17 hydrogen bonds · protein-protein
- A–D · 1604 Ų buried · 19 hydrogen bonds · protein-protein
Compared structures
- 1UMD · 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
- Q5SLR3 · AlphaFold monomer V2.0 prediction for 2-oxoisovalerate dehydrogenase subunit beta (Q5SLR3) · a predicted model of the same protein · chain B against A, TM-score 1.00
- Q5SLR4 · AlphaFold monomer V2.0 prediction for 2-oxoisovalerate dehydrogenase subunit alpha… · a predicted model of the same protein · chain C 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 Q5SLR4
- Every structure of UniProt Q5SLR3
- Elsewhere: RCSB PDB 1UMD · PDBe 1UMD · UniProt Q5SLR4 · UniProt Q5SLR3
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