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Crystal structure of S-adenosylmethionine tRNA ribosyltransferase (TM0574) from Thermotoga maritima at 2.00 A resolution
Analyse Crystal structure of S-adenosylmethionine tRNA ribosyltransferase (TM0574) from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1VKY
- Type
- protein
- Length
- 563 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2
- Source
- Thermotoga maritima
- Molecule
- S-adenosylmethionine:tRNA ribosyltransferase-isomerase
- EC
- 5.-.-.-
- UniProt
- Q9WZ44
- Ligands
- UNL
- Pockets
- 6 · best druggability 0.59
Structure
x-ray diffraction · resolution 2 · 2 distinct chains · 28% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | S-adenosylmethionine:tRNA ribosyltransferase-isomerase (EC 5.-.-.-) | protein | 280 | 29% helix, 33% strand | Q9WZ44 |
| B | S-adenosylmethionine:tRNA ribosyltransferase-isomerase (EC 5.-.-.-) | protein | 283 | 28% helix, 34% strand | Q9WZ44 |
Ligands and binding sites
- UNL · Unknown ligand · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 79 | 0.59 | 0.88 | 20 | empty |
| 2 | 265 | 0.55 | 0.77 | 31 | UNL |
| 3 | 264 | 0.55 | 0.77 | 34 | UNL |
| 4 | 76 | 0.34 | 0.75 | 12 | empty |
| 5 | 63 | 0.33 | 0.76 | 12 | empty |
Interfaces
1 interface between chains.
- A–B · 517 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 1VKY · Crystal structure of S-adenosylmethionine tRNA ribosyltransferase (TM0574) from… · the same entry in another collection · chain A against A, TM-score 1.00
- Q9WZ44 · AlphaFold monomer V2.0 prediction for S-ADENOSYLMETHIONINE:TRNA… · a predicted model of the same protein · chain B against A, TM-score 0.72
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 Q9WZ44
- Elsewhere: RCSB PDB 1VKY · PDBe 1VKY · UniProt Q9WZ44
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