Research workbench
Crystal structure of the catalytic domain of C. glutamicum acef (E2P) in ternary complex with CoA and dihydrolipoamide.
Analyse Crystal structure of the catalytic domain of C. glutamicum acef (E2P) in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6ZZK
- Type
- protein
- Length
- 481 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dihydrolipoyllysine-residue acetyltransferase component of pyruvate dehydrogenase complex
- EC
- 2.3.1.12
- UniProt
- Q8NNJ2
- Ligands
- COA, LPM
- Pockets
- 3 · best druggability 0.74
Structure
x-ray diffraction · 2 distinct chains · 39% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Dihydrolipoyllysine-residue acetyltransferase component of pyruvate dehydrogenase complex (EC 2.3.1.12) | protein | 240 | 39% helix, 24% strand | Q8NNJ2 |
| B | Dihydrolipoyllysine-residue acetyltransferase component of pyruvate dehydrogenase complex (EC 2.3.1.12) | protein | 241 | 39% helix, 26% strand | Q8NNJ2 |
Ligands and binding sites
- COA · Coenzyme A · ligand · 2 copies · chains A, B
- LPM · 6,8-dimercapto-octanoic acid amide · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 918 | 0.74 | 0.78 | 90 | LPM |
| 2 | 479 | 0.64 | 0.77 | 57 | COA |
| 3 | 96 | 0.42 | 0.78 | 23 | COA |
Interfaces
1 interface between chains.
- A–B · 345 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 6ZZK · Crystal structure of the catalytic domain of C. glutamicum AceF (E2p) in ternary complex… · the same entry in another collection · chain A against A, TM-score 1.00
- Q8NNJ2 · AlphaFold monomer V2.0 prediction for dihydrolipoyllysine-residue acetyltransferase… · a predicted model of the same protein · chain A against A, TM-score 0.98
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 Q8NNJ2
- Elsewhere: RCSB PDB 6ZZK · PDBe 6ZZK · UniProt Q8NNJ2
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