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The crystal structure of pyruvate dehydrogenase E1 bound to the peripheral subunit binding domain of E2
Analyse The crystal structure of pyruvate dehydrogenase E1 bound to the peripheral… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- 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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