MolNFT v1 · #63040 · protein
Crystal structure of the pyruvate dehydrogenase (E1P) component of human pyruvate dehydrogenase complex
3EXH · Pyruvate dehydrogenase E1 component subunit alpha, somatic…: “Crystal structure of the pyruvate dehydrogenase (E1P) component of human pyruvate dehydrogenase complex”. X-ray diffraction, 3 ligands (TPP, MN, K), 19 pockets (best…
- 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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