Research workbench
Structure of ynca, a putative acetyltransferase from salmonella typhimurium
Analyse Structure of ynca, a putative acetyltransferase from salmonella typhimurium in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3DR6
- Type
- protein
- Length
- 511 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ynca
- EC
- 2.3.1.-
- Pockets
- 4 · best druggability 0.79
Structure
x-ray diffraction · 3 distinct chains · 35% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ynca (EC 2.3.1.-) | protein | 172 | 35% helix, 34% strand | — |
| B | Ynca (EC 2.3.1.-) | protein | 169 | 36% helix, 34% strand | — |
| C | Ynca (EC 2.3.1.-) | protein | 170 | 34% helix, 34% strand | — |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1153 | 0.79 | 0.81 | 116 | EDO |
| 2 | 404 | 0.63 | 0.77 | 40 | empty |
| 3 | 164 | 0.42 | 0.74 | 27 | empty |
| 4 | 84 | 0.39 | 0.78 | 18 | empty |
Interfaces
2 interfaces between chains.
- A–B · 1711 Ų buried · 38 hydrogen bonds · protein-protein
- A–C · 560 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 modified (engineered).
Compared structures
- 3DR6 · Structure of yncA, a putative ACETYLTRANSFERASE from Salmonella typhimurium · the same entry in another collection · 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
- Elsewhere: RCSB PDB 3DR6 · PDBe 3DR6
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