Research workbench
Crystal structure of the catalytic domain plus N-terminal linker of the acetyltransferase acef (E2P) from corynebacterium glutamicum.
Analyse Crystal structure of the catalytic domain plus N-terminal linker of the… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6ZZL
- Type
- protein
- Length
- 761 residues
- Chains
- 3
- 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
- PO4
- Pockets
- 8 · best druggability 0.82
Structure
x-ray diffraction · 2 distinct chains · 38% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Dihydrolipoyllysine-residue acetyltransferase component of pyruvate dehydrogenase complex (EC 2.3.1.12) | protein | 255 | 38% helix, 25% strand | Q8NNJ2 |
| B, C | Dihydrolipoyllysine-residue acetyltransferase component of pyruvate dehydrogenase complex (EC 2.3.1.12) | protein | 253 | 38% helix, 26% strand | Q8NNJ2 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 241 | 0.82 | 0.95 | 36 | PO4 |
| 2 | 818 | 0.79 | 0.82 | 93 | empty |
| 3 | 535 | 0.74 | 0.82 | 62 | GOL |
| 4 | 548 | 0.72 | 0.80 | 59 | GOL |
| 5 | 481 | 0.71 | 0.81 | 60 | empty |
Interfaces
3 interfaces between chains.
- A–B · 2151 Ų buried · 33 hydrogen bonds · protein-protein
- A–C · 2016 Ų buried · 21 hydrogen bonds · protein-protein
- B–C · 2015 Ų buried · 28 hydrogen bonds · protein-protein
Compared structures
- 6ZZL · Crystal structure of the catalytic domain plus N-terminal linker of the acetyltransferase… · 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 B against A, TM-score 0.99
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 6ZZL · PDBe 6ZZL · UniProt Q8NNJ2
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