MolNFT v1 · #10497 · protein
Crystal structure of archaeosine tRNA-guanine transglycosylase from pyrococcus horikoshii complexed with archaeosine precursor, PREQ0
1IT8: “Crystal structure of archaeosine tRNA-guanine transglycosylase from pyrococcus horikoshii complexed with…”. X-ray diffraction, 3 ligands (PQ0, ZN, MG), 11 pockets (best druggability 0.74). MolNFT v1 #10497 on GenesisL1: 3D…
- PDB
- 1IT8
- Type
- protein
- Length
- 1,154 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Archaeosine tRNA-guanine transglycosylase
- EC
- 2.4.2.29
- UniProt
- O58843
- Ligands
- PQ0, ZN, MG
- Pockets
- 11 · best druggability 0.74
Structure
x-ray diffraction · 1 distinct chain · 41% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Archaeosine tRNA-guanine transglycosylase (EC 2.4.2.29) | protein | 577 | 41% helix, 21% strand | O58843 |
Ligands and binding sites
- PQ0 · 2-amino-4-oxo-4,7-dihydro-3H-pyrrolo[2,3-d]pyrimidine-5-carbonitrile · ligand · chains A
- ZN · Zinc ion · metal · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 393 | 0.74 | 0.84 | 50 | PQ0 |
| 2 | 417 | 0.73 | 0.83 | 50 | empty |
| 3 | 258 | 0.71 | 0.86 | 51 | empty |
| 4 | 201 | 0.57 | 0.80 | 25 | empty |
| 5 | 181 | 0.56 | 0.80 | 26 | empty |
Interfaces
1 interface between chains.
- A–B · 2215 Ų buried · 45 hydrogen bonds · protein-protein
Compared structures
- 1IT8 · Crystal structure of archaeosine tRNA-guanine transglycosylase from Pyrococcus horikoshii… · the same entry in another collection · chain B against B, TM-score 1.00
- O58843 · AlphaFold monomer V2.0 prediction for tRNA-GUANINE(15) transglycosylase (O58843) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 O58843
- Elsewhere: RCSB PDB 1IT8 · PDBe 1IT8 · UniProt O58843
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