Research workbench
Human pyruvate dehydrogenase
Analyse Human pyruvate dehydrogenase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1NI4
- Type
- protein
- Length
- 1,384 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pyruvate dehydrogenase E1 component: alpha subunit; Pyruvate dehydrogenase E1 component…
- EC
- 1.2.4.1
- UniProt
- P08559, P11177
- Ligands
- TPP, MG, K
- Pockets
- 12 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 42% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Pyruvate dehydrogenase E1 component: alpha subunit (EC 1.2.4.1) | protein | 362 | 42% helix, 15% strand | P08559 |
| B, D | Pyruvate dehydrogenase E1 component: beta subunit (EC 1.2.4.1) | protein | 330 | 42% helix, 17% strand | P11177 |
Ligands and binding sites
- TPP · Thiamine diphosphate · ligand · 2 copies · chains A, D, B, C
- MG · Magnesium ion · metal · 2 copies · chains C, A
- K · Potassium ion · metal · 2 copies · chains B, D
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 | 448 | 0.80 | 0.88 | 74 | TPP, MG |
| 2 | 377 | 0.79 | 0.89 | 61 | MG, TPP |
| 3 | 90 | 0.73 | 0.96 | 29 | empty |
| 4 | 62 | 0.70 | 0.97 | 18 | empty |
| 5 | 400 | 0.63 | 0.78 | 35 | empty |
Interfaces
6 interfaces between chains.
- B–D · 2493 Ų buried · 30 hydrogen bonds · protein-protein
- B–C · 1911 Ų buried · 30 hydrogen bonds · protein-protein
- A–D · 1887 Ų buried · 31 hydrogen bonds · protein-protein
- A–B · 1804 Ų buried · 22 hydrogen bonds · protein-protein
- C–D · 1801 Ų buried · 20 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 50 modified (engineered).
Compared structures
- 1NI4 · Human pyruvate dehydrogenase · the same entry in another collection · chain A against A, TM-score 1.00
- P11177 · AlphaFold monomer V2.0 prediction for pyruvate dehydrogenase E1 component subunit beta… · a predicted model of the same protein · chain B against A, TM-score 1.00
- P08559 · AlphaFold monomer V2.0 prediction for pyruvate dehydrogenase E1 component 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 P08559
- Every structure of UniProt P11177
- Elsewhere: RCSB PDB 1NI4 · PDBe 1NI4 · UniProt P08559 · UniProt P11177
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.