Research workbench
E. COLI pyruvate dehydrogenase H407A variant phosphonolactylthiamin diphosphate complex
Analyse E. COLI pyruvate dehydrogenase H407A variant phosphonolactylthiamin diphosphate… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2G28
- 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
- TDK, MG
- Pockets
- 14 · best druggability 0.78
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
- TDK · 3-[(4-amino-2-methylpyrimidin-5-yl)methyl]-2-{(1S)-1-hydroxy-1-[(R)-hydroxy(methoxy)phosphoryl]ethyl}-5-(2-{[(S)-hydroxy(phosphonooxy)phosphoryl]oxy}ethyl)-4-methyl-1,3-thiazol-3-ium · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains B, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 813 | 0.78 | 0.82 | 98 | MG, TDK |
| 2 | 444 | 0.73 | 0.83 | 52 | MG, TDK |
| 3 | 54 | 0.69 | 0.97 | 14 | empty |
| 4 | 208 | 0.69 | 0.86 | 24 | empty |
| 5 | 371 | 0.68 | 0.81 | 40 | empty |
Interfaces
1 interface between chains.
- A–B · 5947 Ų buried · 129 hydrogen bonds · protein-protein
Compared structures
- 2G28 · E. Coli Pyruvate Dehydrogenase H407A variant Phosphonolactylthiamin Diphosphate Complex · the same entry in another collection · chain A against A, TM-score 1.00
- P0AFG8 · AlphaFold monomer V2.0 prediction for pyruvate dehydrogenase E1 component (P0AFG8) · a predicted model of the same protein · chain A 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 P0AFG8
- Elsewhere: RCSB PDB 2G28 · PDBe 2G28 · UniProt P0AFG8
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