MolNFT v1 · #57920 · protein + RNA
Crystal structure of the tias-TRNA(ILE2)-ampcpp-agmatine complex
3AMU · Putative uncharacterized protein: “Crystal structure of the tias-TRNA(ILE2)-ampcpp-agmatine complex”. X-ray diffraction, 2 ligands (APC, AG2), 4 pockets (best druggability 0.82). MolNFT v1 #57920 on GenesisL1: 3D structure, binding…
- PDB
- 3AMU
- Type
- protein + RNA
- Length
- 480 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative uncharacterized protein; RNA (78-mer)
- UniProt
- O28025
- Ligands
- APC, AG2
- Pockets
- 4 · best druggability 0.82
Structure
x-ray diffraction · 2 distinct chains · 25% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Putative uncharacterized protein | protein | 402 | 25% helix, 29% strand | O28025 |
| B | RNA (78-mer) | rna | 78 | — | — |
Ligands and binding sites
- APC · Diphosphomethylphosphonic acid adenosyl ester · ligand · chains A, B
- AG2 · Agmatine · ligand · chains A, B
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 | 1105 | 0.82 | 0.84 | 97 | APC, AG2 |
| 2 | 580 | 0.65 | 0.77 | 37 | empty |
| 3 | 96 | 0.34 | 0.73 | 21 | empty |
| 4 | 65 | 0.29 | 0.75 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 1715 Ų buried · 40 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 1 modified (phosphorylation).
Compared structures
- 3AMU · Crystal structure of the TiaS-tRNA(Ile2)-AMPCPP-agmatine complex · the same entry in another collection · chain A against A, 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 A 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 3AMU · PDBe 3AMU · UniProt O28025
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