Research workbench
E. COLI pyruvate dehydrogenase complex E1 component E571A mutant
Analyse E. COLI pyruvate dehydrogenase complex E1 component E571A mutant in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3LPL
- 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
- P0AFG9
- Ligands
- TPP, MG, PO4
- Pockets
- 16 · best druggability 0.73
Structure
x-ray diffraction · 1 distinct chain · 45% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Pyruvate dehydrogenase E1 component (EC 1.2.4.1) | protein | 801 | 45% helix, 12% strand | P0AFG9 |
Ligands and binding sites
- TPP · Thiamine diphosphate · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
- PO4 · Phosphate ion · ion · 2 copies · chains A, B
- EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 63 | 0.73 | 0.97 | 14 | empty |
| 2 | 451 | 0.71 | 0.81 | 61 | TPP, MG |
| 3 | 450 | 0.71 | 0.81 | 77 | TPP |
| 4 | 216 | 0.69 | 0.86 | 24 | empty |
| 5 | 56 | 0.69 | 0.96 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 5961 Ų buried · 106 hydrogen bonds · protein-protein
Compared structures
- 3LPL · E. coli pyruvate dehydrogenase complex E1 component E571A mutant · the same entry in another collection · chain A against A, TM-score 1.00
- P0AFG9 · AlphaFold monomer V2.0 prediction for pyruvate dehydrogenase E1 component (P0AFG9) · 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 P0AFG9
- Elsewhere: RCSB PDB 3LPL · PDBe 3LPL · UniProt P0AFG9
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