Research workbench
Crystal structure of the pyruvate dehydrogenase (E1P) component of human pyruvate dehydrogenase complex with the subunit-binding domain (sbd) of E2P, but sbd cannot be modeled into the electron density
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
- 3EXI
- Type
- protein
- Length
- 661 residues
- Chains
- 2
- 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
- K, CL
- Pockets
- 4 · best druggability 0.69
Structure
x-ray diffraction · 2 distinct chains · 41% helix, 16% 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 | 332 | 41% helix, 16% strand | P08559 |
| B | Pyruvate dehydrogenase E1 component subunit beta, mitochondrial (EC 1.2.4.1) | protein | 329 | 42% helix, 17% strand | P11177 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 83 | 0.69 | 0.93 | 19 | empty |
| 2 | 412 | 0.59 | 0.75 | 45 | empty |
| 3 | 89 | 0.46 | 0.81 | 16 | empty |
| 4 | 51 | 0.26 | 0.74 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 1812 Ų buried · 23 hydrogen bonds · protein-protein
Compared structures
- 3EXI · Crystal structure of the pyruvate dehydrogenase (E1p) component of human pyruvate… · the same entry in another collection · chain A against A, 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 A against A, TM-score 0.97
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 3EXI · PDBe 3EXI · UniProt P08559 · UniProt P11177
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