Research workbench
Structure of the GTP-binding protein TrmE from Thermotoga maritima complexed with 5-formyl-THF
Analyse Structure of the GTP-binding protein TrmE from Thermotoga maritima complexed… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1XZQ
- Type
- protein
- Length
- 566 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.9
- Source
- Thermotoga maritima
- Molecule
- Probable tRNA modification GTPase trmE
- UniProt
- Q9WYA4
- Ligands
- FON
- Pockets
- 6 · best druggability 0.72
Structure
x-ray diffraction · resolution 2.9 · 2 distinct chains · 42% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Probable tRNA modification GTPase trmE | protein | 449 | 47% helix, 17% strand | Q9WYA4 |
| B | Probable tRNA modification GTPase trmE | protein | 117 | 23% helix, 36% strand | Q9WYA4 |
Ligands and binding sites
- FON · N-{[4-({[(6R)-2-amino-5-formyl-4-oxo-1,4,5,6,7,8-hexahydropteridin-6-yl]methyl}amino)phenyl]carbonyl}-L-glutamic acid · 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 | 377 | 0.72 | 0.83 | 38 | FON |
| 2 | 242 | 0.63 | 0.82 | 25 | FON |
| 3 | 189 | 0.50 | 0.77 | 25 | empty |
| 4 | 121 | 0.42 | 0.76 | 16 | empty |
| 5 | 83 | 0.40 | 0.78 | 31 | empty |
Interfaces
1 interface between chains.
- A–B · 1511 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 1XZQ · Structure of the GTP-binding protein trme from thermotoga maritima complexed with… · the same entry in another collection · chain A against A, TM-score 1.00
- Q9WYA4 · AlphaFold monomer V2.0 prediction for tRNA modification GTPase mnme (Q9WYA4) · a predicted model of the same protein · chain B against A, TM-score 0.98
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 Q9WYA4
- Elsewhere: RCSB PDB 1XZQ · PDBe 1XZQ · UniProt Q9WYA4
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.