Research workbench
E. COLI pyruvate dehydrogenase
Analyse E. COLI pyruvate dehydrogenase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2IEA
- Type
- protein
- Length
- 1,602 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pyruvate dehydrogenase E1 component
- EC
- 1.2.4.1
- UniProt
- P0AFG8
- Ligands
- TPP, MG
- Pockets
- 15 · best druggability 0.70
Structure
x-ray diffraction · 1 distinct chain · 44% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Pyruvate dehydrogenase E1 component (EC 1.2.4.1) | protein | 801 | 44% helix, 12% strand | P0AFG8 |
Ligands and binding sites
- TPP · Thiamine diphosphate · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 400 | 0.70 | 0.82 | 59 | MG, TPP |
| 2 | 375 | 0.70 | 0.82 | 48 | TPP |
| 3 | 354 | 0.69 | 0.82 | 37 | empty |
| 4 | 367 | 0.68 | 0.81 | 41 | empty |
| 5 | 342 | 0.66 | 0.81 | 43 | empty |
Interfaces
1 interface between chains.
- A–B · 5866 Ų buried · 120 hydrogen bonds · protein-protein
Compared structures
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 P0AFG8
- Elsewhere: RCSB PDB 2IEA · PDBe 2IEA · UniProt P0AFG8
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