Research workbench
TRNA-guanine transglycosylase C158S/C281S/Y330C/H333A mutant in complex with rac-trans-4,4-difluorocyclopentane-1,2-diol
Analyse TRNA-guanine transglycosylase C158S/C281S/Y330C/H333A mutant in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7A6D
- Type
- protein
- Length
- 372 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Queuine tRNA-ribosyltransferase
- EC
- 2.4.2.29
- UniProt
- P28720
- Ligands
- R1E, RGN, ZN
- Pockets
- 3 · best druggability 0.66
Structure
x-ray diffraction · 1 distinct chain · 46% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Queuine tRNA-ribosyltransferase (EC 2.4.2.29) | protein | 372 | 46% helix, 19% strand | P28720 |
Ligands and binding sites
- R1E · trans-4,4-difluorocyclopentane-1,2-diol · ligand · chains A
- RGN · (1~{R},2~{R})-4,4-bis(fluoranyl)cyclopentane-1,2-diol · ligand · chains A
- ZN · Zinc ion · metal · chains A
- GOL · Glycerol · additive · 3 copies · chains A
- EDO · 1,2-ethanediol · additive · 2 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, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 228 | 0.66 | 0.84 | 35 | empty |
| 2 | 111 | 0.44 | 0.77 | 18 | GOL, R1E |
| 3 | 58 | 0.42 | 0.82 | 12 | EDO |
Compared structures
- 7A6D · tRNA-guanine transglycosylase C158S/C281S/Y330C/H333A mutant in complex with… · 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
- Every structure of UniProt P28720
- Elsewhere: RCSB PDB 7A6D · PDBe 7A6D · UniProt P28720
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