Research workbench
Chemical trapping and crystal structure of a catalytic tRNA guanine transglycosylase covalent intermediate
Analyse Chemical trapping and crystal structure of a catalytic tRNA guanine… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1Q2S
- Type
- protein + RNA
- Length
- 1,536 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5'-R(*AP*GP*CP*AP*CP*GP*GP*CP*UP*(PQ1) P*UP*AP*AP*AP*CP*CP*GP*UP*GP*C)-3'; Queuine…
- EC
- 2.4.2.29
- UniProt
- P28720
- Ligands
- 9DG, ZN
- Pockets
- 18 · best druggability 0.76
Structure
x-ray diffraction · 3 distinct chains · 45% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| E, F | 5'-R(*AP*GP*CP*AP*CP*GP*GP*CP*UP*(PQ1) P*UP*AP*AP*AP*CP*CP*GP*UP*GP*C)-3' | rna | 20 | — | — |
| A, C | Queuine tRNA-ribosyltransferase (EC 2.4.2.29) | protein | 376 | 47% helix, 20% strand | P28720 |
| B, D | Queuine tRNA-ribosyltransferase (EC 2.4.2.29) | protein | 372 | 44% helix, 18% strand | P28720 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 901 | 0.76 | 0.79 | 71 | empty |
| 2 | 187 | 0.66 | 0.85 | 29 | empty |
| 3 | 209 | 0.65 | 0.84 | 34 | empty |
| 4 | 384 | 0.60 | 0.76 | 46 | empty |
| 5 | 418 | 0.60 | 0.76 | 42 | empty |
Interfaces
9 interfaces between chains.
- C–D · 1732 Ų buried · 15 hydrogen bonds · protein-protein
- A–B · 1709 Ų buried · 16 hydrogen bonds · protein-protein
- E–A · 1505 Ų buried · 52 hydrogen bonds · protein-nucleic
- F–C · 1379 Ų buried · 42 hydrogen bonds · protein-nucleic
- F–D · 321 Ų buried · 11 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 1 modified (nucleotide modification).
Compared structures
- 1Q2S · Chemical trapping and crystal structure of a catalytic tRNA guanine transglycosylase… · the same entry in another collection · chain E against E, 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 1Q2S · PDBe 1Q2S · UniProt P28720
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