MolNFT v1 · #25870 · protein
The crystal structure of pyruvate dehydrogenase E1 bound to the peripheral subunit binding domain of E2
1W85 · Pyruvate dehydrogenase E1 component, alpha subunit: “The crystal structure of pyruvate dehydrogenase E1 bound to the peripheral subunit binding domain of E2”. X-ray diffraction, 3 ligands (TPP, MG, K), 20 pockets (best druggability…
- PDB
- 1W85
- Type
- protein
- Length
- 2,809 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, K
- Pockets
- 20 · best druggability 0.80
Structure
x-ray diffraction · 7 distinct chains · 50% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Pyruvate dehydrogenase E1 component, alpha subunit (EC 1.2.4.1) | protein | 358 | 51% helix, 10% strand | P21873 |
| B, D, F, H | Pyruvate dehydrogenase E1 component, beta subunit (EC 1.2.4.1) | protein | 324 | 40% helix, 19% strand | P21874 |
| C | Pyruvate dehydrogenase E1 component, alpha subunit (EC 1.2.4.1) | protein | 365 | 53% helix, 10% strand | P21873 |
| E | Pyruvate dehydrogenase E1 component, alpha subunit (EC 1.2.4.1) | protein | 350 | 53% helix, 10% strand | P21873 |
| G | Pyruvate dehydrogenase E1 component, alpha subunit (EC 1.2.4.1) | protein | 364 | 51% helix, 10% strand | P21873 |
| I | Dihydrolipoyllysine-residue acetyltransferase component of pyruvate (EC 2.3.1.12) | protein | 42 | 48% helix, 0% strand | P11961 |
| J | Dihydrolipoyllysine-residue acetyltransferase component of pyruvate (EC 2.3.1.12) | protein | 34 | 47% 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 · 6 copies · chains A, B, C, E, G
- K · Potassium ion · metal · 4 copies · chains B, D, F, H
- PEG · Di(hydroxyethyl)ether · additive · 3 copies · chains A, B, C, D, 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, 16 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 314 | 0.80 | 0.91 | 59 | MG, TPP |
| 2 | 346 | 0.79 | 0.89 | 58 | MG, TPP |
| 3 | 99 | 0.75 | 0.96 | 25 | empty |
| 4 | 409 | 0.75 | 0.85 | 71 | MG, TPP |
| 5 | 556 | 0.75 | 0.82 | 69 | MG, TPP |
Interfaces
16 interfaces between chains.
- B–D · 2175 Ų buried · 39 hydrogen bonds · protein-protein
- F–H · 2152 Ų buried · 35 hydrogen bonds · protein-protein
- A–C · 1911 Ų buried · 23 hydrogen bonds · protein-protein
- E–G · 1891 Ų buried · 21 hydrogen bonds · protein-protein
- E–F · 1804 Ų buried · 26 hydrogen bonds · protein-protein
Compared structures
- 1W85 · The crystal structure of pyruvate dehydrogenase E1 bound to the peripheral subunit… · 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
- P21873 · AlphaFold monomer V2.0 prediction for pyruvate dehydrogenase E1 component subunit alpha… · a predicted model of the same protein · chain E 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 P21873
- Every structure of UniProt P21874
- Every structure of UniProt P11961
- Elsewhere: RCSB PDB 1W85 · PDBe 1W85 · UniProt P21873 · UniProt P21874 · UniProt P11961
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