MolNFT v1 · #142814 · protein
Crystal structure of agmatine-amppcp-mg complexed tias (TRNAILE2 agmatidine synthetase)
6AGG · TRNA(ILE2) 2-agmatinylcytidine synthetase tias: “Crystal structure of agmatine-amppcp-mg complexed tias (TRNAILE2 agmatidine synthetase)”. X-ray diffraction, 5 ligands (ACP, AG2, MG), 4 pockets (best druggability 0.76). MolNFT v1…
- PDB
- 6AGG
- 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, AG2, MG, ZN, NH4
- Pockets
- 4 · best druggability 0.76
Structure
x-ray diffraction · 1 distinct chain · 25% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| Z | TRNA(ILE2) 2-agmatinylcytidine synthetase tias (EC 6.3.4.22) | protein | 420 | 25% helix, 31% strand | O28025 |
Ligands and binding sites
- ACP · Phosphomethylphosphonic acid adenylate ester · ligand · chains Z
- AG2 · Agmatine · ligand · chains Z
- MG · Magnesium ion · metal · 2 copies · chains Z
- ZN · Zinc ion · metal · chains Z
- NH4 · Ammonium ion · ion · chains Z
- ACT · Acetate ion · additive · 2 copies · chains Z
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 | 634 | 0.76 | 0.82 | 68 | ACP, AG2 |
| 2 | 158 | 0.64 | 0.86 | 32 | empty |
| 3 | 77 | 0.31 | 0.74 | 18 | ACT |
| 4 | 50 | 0.31 | 0.77 | 11 | empty |
Modifications
Observed in the structure: 1 modified (phosphorylation).
Compared structures
- 6AGG · Crystal structure of agmatine-AMPPCP-Mg complexed TiaS (tRNAIle2 agmatidine synthetase) · 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 6AGG · PDBe 6AGG · UniProt O28025
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