Research workbench
Crystal structure of the pyruvate dehydrogenase (E1P) component of human pyruvate dehydrogenase complex
Analyse Crystal structure of the pyruvate dehydrogenase (E1P) component of human… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3EXH
- Type
- protein
- Length
- 2,730 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial; Pyruvate…
- EC
- 1.2.4.1
- UniProt
- P08559, P11177
- Ligands
- TPP, MN, K
- Pockets
- 19 · best druggability 0.79
Structure
x-ray diffraction · 4 distinct chains · 43% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Pyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial (EC 1.2.4.1) | protein | 359 | 43% helix, 14% strand | P08559 |
| B, D, F, H | Pyruvate dehydrogenase E1 component subunit beta, mitochondrial (EC 1.2.4.1) | protein | 329 | 41% helix, 17% strand | P11177 |
| C, G | Pyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial (EC 1.2.4.1) | protein | 362 | 44% helix, 15% strand | P08559 |
| E | Pyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial (EC 1.2.4.1) | protein | 331 | 43% helix, 15% strand | P08559 |
Ligands and binding sites
- TPP · Thiamine diphosphate · ligand · 4 copies · chains A, D, B, C, E, H, F, G
- MN · Manganese (II) ion · metal · 4 copies · chains A, C, E, G
- K · Potassium ion · metal · 4 copies · chains D, B, H, F
- GOL · Glycerol · additive · 5 copies · chains C, D, A, B, G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 15 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 381 | 0.79 | 0.88 | 68 | MN, TPP |
| 2 | 344 | 0.79 | 0.89 | 60 | MN, TPP |
| 3 | 722 | 0.78 | 0.83 | 84 | TPP |
| 4 | 86 | 0.74 | 0.96 | 30 | empty |
| 5 | 90 | 0.73 | 0.96 | 27 | empty |
Interfaces
16 interfaces between chains.
- F–H · 2536 Ų buried · 29 hydrogen bonds · protein-protein
- B–D · 2519 Ų buried · 29 hydrogen bonds · protein-protein
- A–D · 1948 Ų buried · 26 hydrogen bonds · protein-protein
- B–C · 1908 Ų buried · 31 hydrogen bonds · protein-protein
- F–G · 1903 Ų buried · 28 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (phosphorylation).
Compared structures
- 3EXH · Crystal structure of the pyruvate dehydrogenase (E1p) component of human pyruvate… · the same entry in another collection · chain H against H, 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 C 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 3EXH · PDBe 3EXH · UniProt P08559 · UniProt P11177
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