MolNFT v1 · #23007 · RNA
Crystallographic and biochemical investigation of the LEAD(II)- catalyzed hydrolysis of yeast phenylalanine tRNA
1TN1 · Trnaphe: “Crystallographic and biochemical investigation of the LEAD(II)- catalyzed hydrolysis of yeast phenylalanine…”. X-ray diffraction, 3 ligands (SPM, MG, PB), 3 pockets (best druggability 0.60). MolNFT v1 #23007 on GenesisL1…
- PDB
- 1TN1
- Type
- RNA
- Length
- 76 nucleotides
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Trnaphe
- Ligands
- SPM, MG, PB
- Pockets
- 3 · best druggability 0.60
Structure
x-ray diffraction · 1 distinct chain.
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Trnaphe | rna | 76 | — | — |
Ligands and binding sites
- SPM · Spermine · ligand · chains A
- MG · Magnesium ion · metal · 5 copies · chains A
- PB · Lead (II) ion · metal · 3 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 527 | 0.60 | 0.75 | 31 | empty |
| 2 | 390 | 0.60 | 0.77 | 22 | SPM, PB |
| 3 | 53 | 0.27 | 0.75 | 8 | MG |
Modifications
Observed in the structure: 14 modified (nucleotide modification).
Compared structures
- 1TN1 · Crystallographic and biochemical investigation of the LEAD(II)-catalyzed hydrolysis of… · 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 1TN1 · PDBe 1TN1
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