MolNFT v1 · #18879 · protein + RNA
Chemical trapping and crystal structure of a catalytic tRNA guanine transglycosylase covalent intermediate
1Q2R · RNA (5'-R(*AP*GP*CP*AP*CP*GP*GP*CP*UP*(N)…: “Chemical trapping and crystal structure of a catalytic tRNA guanine transglycosylase covalent intermediate”. X-ray diffraction, 2 ligands (9DG, ZN), 14 pockets (best druggability 0.74).…
- PDB
- 1Q2R
- Type
- protein + RNA
- Length
- 1,536 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RNA (5'-R(*AP*GP*CP*AP*CP*GP*GP*CP*UP*(N) P*UP*AP*AP*AP*CP*CP*GP*UP*GP*C)-3'); Queuine…
- EC
- 2.4.2.29
- UniProt
- P28720
- Ligands
- 9DG, ZN
- Pockets
- 14 · best druggability 0.74
Structure
x-ray diffraction · 3 distinct chains · 47% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| E, F | RNA (5'-R(*AP*GP*CP*AP*CP*GP*GP*CP*UP*(N) 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 | 48% helix, 20% strand | P28720 |
| B, D | Queuine tRNA-ribosyltransferase (EC 2.4.2.29) | protein | 372 | 46% helix, 19% strand | P28720 |
Ligands and binding sites
- 9DG · 9-deazaguanine · ligand · 4 copies · chains E, A, B, F, C, D
- ZN · Zinc ion · metal · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 784 | 0.74 | 0.80 | 58 | empty |
| 2 | 326 | 0.71 | 0.84 | 58 | 9DG |
| 3 | 447 | 0.70 | 0.81 | 70 | 9DG |
| 4 | 688 | 0.67 | 0.76 | 69 | empty |
| 5 | 84 | 0.56 | 0.87 | 26 | 9DG |
Interfaces
9 interfaces between chains.
- A–B · 1732 Ų buried · 19 hydrogen bonds · protein-protein
- C–D · 1731 Ų buried · 20 hydrogen bonds · protein-protein
- E–A · 1358 Ų buried · 51 hydrogen bonds · protein-nucleic
- F–C · 1353 Ų buried · 51 hydrogen bonds · protein-nucleic
- E–F · 242 Ų buried · 12 hydrogen bonds · nucleic-nucleic
Compared structures
- 1Q2R · 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 1Q2R · PDBe 1Q2R · UniProt P28720
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