Research workbench
The crystal structure of pyruvate dehydrogenase E1(D180N,E183Q) bound to the peripheral subunit binding domain of E2
Analyse The crystal structure of pyruvate dehydrogenase E1(D180N,E183Q) bound to the… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1W88
- Type
- protein
- Length
- 2,699 residues
- Chains
- 10
- 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, 2.3.1.12
- UniProt
- P21873, P21874, P11961
- Ligands
- TPP, MG
- Pockets
- 20 · best druggability 0.81
Structure
x-ray diffraction · 9 distinct chains · 46% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Pyruvate dehydrogenase E1 component, alpha subunit (EC 1.2.4.1) | protein | 340 | 51% helix, 11% strand | P21873 |
| B, D | Pyruvate dehydrogenase E1 component, beta subunit (EC 1.2.4.1) | protein | 324 | 41% helix, 20% strand | P21874 |
| C | Pyruvate dehydrogenase E1 component, alpha subunit (EC 1.2.4.1) | protein | 343 | 51% helix, 11% strand | P21873 |
| E | Pyruvate dehydrogenase E1 component, alpha subunit (EC 1.2.4.1) | protein | 328 | 51% helix, 10% strand | P21873 |
| F | Pyruvate dehydrogenase E1 component, beta subunit (EC 1.2.4.1) | protein | 310 | 39% helix, 20% strand | P21874 |
| G | Pyruvate dehydrogenase E1 component, alpha subunit (EC 1.2.4.1) | protein | 331 | 51% helix, 10% strand | P21873 |
| H | Pyruvate dehydrogenase E1 component, beta subunit (EC 1.2.4.1) | protein | 317 | 38% helix, 20% strand | P21874 |
| I | Dihydrolipoyllysine-residue acetyltransferase component of pyruvate (EC 2.3.1.12) | protein | 40 | 48% helix, 0% strand | P11961 |
| J | Dihydrolipoyllysine-residue acetyltransferase component of pyruvate (EC 2.3.1.12) | protein | 42 | 45% helix, 0% strand | P11961 |
Ligands and binding sites
- TPP · Thiamine diphosphate · ligand · 4 copies · chains A, D, B, C, E, H, F, G
- MG · Magnesium ion · metal · 4 copies · chains A, C, E, G
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1182 | 0.81 | 0.82 | 77 | MG, TPP |
| 2 | 149 | 0.77 | 0.94 | 28 | empty |
| 3 | 276 | 0.74 | 0.88 | 41 | empty |
| 4 | 117 | 0.72 | 0.93 | 29 | empty |
| 5 | 537 | 0.72 | 0.80 | 48 | TPP |
Interfaces
18 interfaces between chains.
- B–D · 2184 Ų buried · 39 hydrogen bonds · protein-protein
- F–H · 2079 Ų buried · 30 hydrogen bonds · protein-protein
- E–F · 1812 Ų buried · 28 hydrogen bonds · protein-protein
- G–H · 1799 Ų buried · 25 hydrogen bonds · protein-protein
- A–B · 1794 Ų buried · 25 hydrogen bonds · protein-protein
Compared structures
- 1W88 · The crystal structure of pyruvate dehydrogenase E1(D180N,E183Q) bound to the peripheral… · the same entry in another collection · chain J against J, TM-score 1.00
- P21874 · 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
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 P21873
- Every structure of UniProt P21874
- Every structure of UniProt P11961
- Elsewhere: RCSB PDB 1W88 · PDBe 1W88 · UniProt P21873 · UniProt P21874 · UniProt P11961
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.