Research workbench
Restrained refinement of the monoclinic form of yeast phenylalanine transfer RNA. temperature factors and dynamics, coordinated waters, and base-pair propeller twist angles
Analyse Restrained refinement of the monoclinic form of yeast phenylalanine transfer… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1TRA
- Type
- RNA
- Length
- 76 nucleotides
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Trnaphe
- Ligands
- MG
- Pockets
- 3 · best druggability 0.61
Structure
x-ray diffraction · 1 distinct chain.
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Trnaphe | rna | 76 | — | — |
Ligands and binding sites
- MG · Magnesium ion · metal · 5 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 | 545 | 0.61 | 0.75 | 31 | empty |
| 2 | 392 | 0.57 | 0.76 | 22 | MG |
| 3 | 50 | 0.30 | 0.77 | 10 | empty |
Modifications
Observed in the structure: 14 modified (nucleotide modification).
Compared structures
- 1TRA · Restrained refinement of the monoclinic form of yeast phenylalanine transfer RNA.… · 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 1TRA · PDBe 1TRA
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