Research workbench
Crystal structure of TRNA(MET) cytidine acetyltransferase
Analyse Crystal structure of TRNA(MET) cytidine acetyltransferase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2ZPA
- Type
- protein
- Length
- 1,320 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Uncharacterized protein ypfi
- EC
- 2.3.1.-
- UniProt
- P76562
- Ligands
- ACO, ADP, SO4
- Pockets
- 13 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 43% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Uncharacterized protein ypfi (EC 2.3.1.-) | protein | 658 | 44% helix, 17% strand | P76562 |
| B | Uncharacterized protein ypfi (EC 2.3.1.-) | protein | 662 | 42% helix, 15% strand | P76562 |
Ligands and binding sites
- ACO · Acetyl coenzyme *A · ligand · 2 copies · chains A, B
- ADP · Adenosine-5'-diphosphate · ligand · chains A
- SO4 · Sulfate ion · ion · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 716 | 0.78 | 0.83 | 83 | SO4 |
| 2 | 785 | 0.78 | 0.82 | 72 | ADP |
| 3 | 935 | 0.76 | 0.79 | 87 | ACO |
| 4 | 858 | 0.75 | 0.79 | 74 | ACO |
| 5 | 259 | 0.52 | 0.75 | 26 | empty |
Interfaces
1 interface between chains.
- A–B · 187 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 21 modified (engineered).
Compared structures
- 2ZPA · Crystal Structure of tRNA(Met) Cytidine Acetyltransferase · the same entry in another collection · chain A against A, TM-score 1.00
- P76562 · AlphaFold monomer V2.0 prediction for TRNA(MET) cytidine acetyltransferase tmca (P76562) · a predicted model of the same protein · chain A 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 P76562
- Elsewhere: RCSB PDB 2ZPA · PDBe 2ZPA · UniProt P76562
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