Research workbench
Human pyruvate dehydrogenase complex E1 component V138M mutation
Analyse Human pyruvate dehydrogenase complex E1 component V138M mutation in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6CER
- Type
- protein
- Length
- 2,661 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, MG
- Pockets
- 18 · best druggability 0.77
Structure
x-ray diffraction · 6 distinct chains · 42% 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 | 342 | 43% helix, 15% strand | P08559 |
| B, F | Pyruvate dehydrogenase E1 component subunit beta, mitochondrial (EC 1.2.4.1) | protein | 330 | 41% helix, 18% strand | P11177 |
| C | Pyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial (EC 1.2.4.1) | protein | 328 | 42% helix, 15% strand | P08559 |
| D, H | Pyruvate dehydrogenase E1 component subunit beta, mitochondrial (EC 1.2.4.1) | protein | 331 | 41% helix, 18% strand | P11177 |
| E | Pyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial (EC 1.2.4.1) | protein | 340 | 42% helix, 15% strand | P08559 |
| G | Pyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial (EC 1.2.4.1) | protein | 329 | 42% helix, 16% strand | P08559 |
Ligands and binding sites
- TPP · Thiamine diphosphate · ligand · 4 copies · chains A, D, B, C, E, H, F, G
- MG · Magnesium ion · metal · 2 copies · chains E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 878 | 0.77 | 0.80 | 104 | TPP |
| 2 | 89 | 0.73 | 0.96 | 28 | empty |
| 3 | 477 | 0.67 | 0.79 | 63 | TPP |
| 4 | 167 | 0.66 | 0.86 | 37 | empty |
| 5 | 424 | 0.65 | 0.78 | 39 | empty |
Interfaces
15 interfaces between chains.
- B–D · 2528 Ų buried · 29 hydrogen bonds · protein-protein
- F–H · 2523 Ų buried · 32 hydrogen bonds · protein-protein
- A–B · 1812 Ų buried · 22 hydrogen bonds · protein-protein
- C–D · 1783 Ų buried · 20 hydrogen bonds · protein-protein
- G–H · 1780 Ų buried · 21 hydrogen bonds · protein-protein
Compared structures
- 6CER · Human pyruvate dehydrogenase complex E1 component V138M mutation · 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 6CER · PDBe 6CER · UniProt P08559 · UniProt P11177
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