MolNFT v1 · #106329 · protein
Crystal structure of tRNA fluorescent labeling enzyme
4RVZ · TRNA(ILE2) 2-agmatinylcytidine synthetase tias: “Crystal structure of tRNA fluorescent labeling enzyme”. X-ray diffraction, 4 ligands (ACP, ZNN, MG), 5 pockets (best druggability 0.76). MolNFT v1 #106329 on GenesisL1: 3D structure…
- PDB
- 4RVZ
- Type
- protein
- Length
- 420 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- TRNA(ILE2) 2-agmatinylcytidine synthetase tias
- EC
- 6.3.4.22
- UniProt
- O28025
- Ligands
- ACP, ZNN, MG, ZN
- Pockets
- 5 · best druggability 0.76
Structure
x-ray diffraction · 1 distinct chain · 26% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| Z | TRNA(ILE2) 2-agmatinylcytidine synthetase tias (EC 6.3.4.22) | protein | 420 | 26% helix, 32% strand | O28025 |
Ligands and binding sites
- ACP · Phosphomethylphosphonic acid adenylate ester · ligand · chains Z
- ZNN · N-(4-aminobutyl)-2-azidoacetamide · ligand · chains Z
- MG · Magnesium ion · metal · 2 copies · chains Z
- ZN · Zinc ion · metal · chains Z
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 570 | 0.76 | 0.83 | 68 | ACP, MG, ZNN |
| 2 | 117 | 0.68 | 0.90 | 28 | empty |
| 3 | 54 | 0.43 | 0.83 | 17 | empty |
| 4 | 71 | 0.36 | 0.77 | 15 | empty |
| 5 | 76 | 0.30 | 0.73 | 16 | empty |
Modifications
Observed in the structure: 1 modified (phosphorylation).
Compared structures
- 4RVZ · Crystal structure of tRNA fluorescent labeling enzyme · the same entry in another collection · chain Z against Z, TM-score 1.00
- O28025 · AlphaFold monomer V2.0 prediction for TRNA(ILE2) 2-agmatinylcytidine synthetase tias… · a predicted model of the same protein · chain Z against A, TM-score 0.97
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 O28025
- Elsewhere: RCSB PDB 4RVZ · PDBe 4RVZ · UniProt O28025
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