Research workbench
E. COLI pyruvate dehydrogenase complex E1 E235A mutant with high tdp concentration
Analyse E. COLI pyruvate dehydrogenase complex E1 E235A mutant with high tdp… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3LQ4
- 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
- 15 · best druggability 0.76
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 | 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 · chains A
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 | 783 | 0.76 | 0.80 | 104 | TPP, MG, PO4 |
| 2 | 60 | 0.72 | 0.97 | 14 | empty |
| 3 | 482 | 0.70 | 0.81 | 60 | TPP, MG |
| 4 | 235 | 0.70 | 0.86 | 25 | empty |
| 5 | 362 | 0.67 | 0.81 | 40 | empty |
Interfaces
1 interface between chains.
- A–B · 5878 Ų buried · 94 hydrogen bonds · protein-protein
Compared structures
- 3LQ4 · E. coli pyruvate dehydrogenase complex E1 E235A mutant with high TDP concentration · 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 3LQ4 · PDBe 3LQ4 · UniProt P0AFG9
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