Research workbench
Snapshots of catalysis in the E1 subunit of the pyruvate dehydrogenase multi-enzyme complex
Analyse Snapshots of catalysis in the E1 subunit of the pyruvate dehydrogenase… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3DVA
- Type
- protein
- Length
- 2,827 residues
- Chains
- 10
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pyruvate dehydrogenase E1 component subunit alpha; Pyruvate dehydrogenase E1 component…
- EC
- 1.2.4.1, 2.3.1.12
- UniProt
- P21873, P21874, P11961
- Ligands
- TPW, MG, K
- Pockets
- 20 · best druggability 0.82
Structure
x-ray diffraction · 5 distinct chains · 45% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, G | Pyruvate dehydrogenase E1 component subunit alpha (EC 1.2.4.1) | protein | 365 | 49% helix, 10% strand | P21873 |
| B, D, F, H | Pyruvate dehydrogenase E1 component subunit beta (EC 1.2.4.1) | protein | 324 | 38% helix, 19% strand | P21874 |
| E | Pyruvate dehydrogenase E1 component subunit alpha (EC 1.2.4.1) | protein | 354 | 51% helix, 10% strand | P21873 |
| I | Dihydrolipoyllysine-residue acetyltransferase component of pyruvate dehydrogenase complex (EC 2.3.1.12) | protein | 42 | 29% helix, 0% strand | P11961 |
| J | Dihydrolipoyllysine-residue acetyltransferase component of pyruvate dehydrogenase complex (EC 2.3.1.12) | protein | 40 | 30% helix, 0% strand | P11961 |
Ligands and binding sites
- TPW · 2-{4-[(4-amino-2-methylpyrimidin-5-yl)methyl]-3-methylthiophen-2-yl}ethyl trihydrogen diphosphate · ligand · 4 copies · chains A, D, B, C, E, H, F, G
- MG · Magnesium ion · metal · 6 copies · chains A, C, E, F, G
- 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
20 pockets found on a 1 Å grid, 17 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 652 | 0.82 | 0.86 | 75 | TPW |
| 2 | 442 | 0.81 | 0.89 | 61 | TPW |
| 3 | 410 | 0.81 | 0.89 | 59 | MG, TPW |
| 4 | 526 | 0.78 | 0.85 | 70 | TPW, MG |
| 5 | 995 | 0.78 | 0.80 | 89 | empty |
Interfaces
17 interfaces between chains.
- F–H · 2140 Ų buried · 36 hydrogen bonds · protein-protein
- B–D · 2130 Ų buried · 40 hydrogen bonds · protein-protein
- A–C · 1980 Ų buried · 25 hydrogen bonds · protein-protein
- E–G · 1942 Ų buried · 24 hydrogen bonds · protein-protein
- G–H · 1819 Ų buried · 24 hydrogen bonds · protein-protein
Compared structures
- 3DVA · Snapshots of catalysis in the E1 subunit of the pyruvate dehydrogenase multi-enzyme… · 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 3DVA · PDBe 3DVA · UniProt P21873 · UniProt P21874 · UniProt P11961
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