Research workbench
Dissecting the roles of a strictly conserved tyrosine in substrate recognition and catalysis by pseudouridine 55 synthase
Analyse Dissecting the roles of a strictly conserved tyrosine in substrate recognition… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2AB4
- Type
- protein + RNA
- Length
- 320 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5'-R(*CP*CP*AP*CP*GP*GP*UP*(FHU) P*CP*GP*AP*AP*UP*CP*CP*GP*UP*GP*GP*C)-3'; TRNA…
- EC
- 5.4.99.-
- UniProt
- Q9WZW0
- Ligands
- ZN
- Pockets
- 4 · best druggability 0.49
Structure
x-ray diffraction · 2 distinct chains · 21% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | 5'-R(*CP*CP*AP*CP*GP*GP*UP*(FHU) P*CP*GP*AP*AP*UP*CP*CP*GP*UP*GP*GP*C)-3' | rna | 20 | — | — |
| A | TRNA pseudouridine synthase B (EC 5.4.99.-) | protein | 300 | 21% helix, 35% strand | Q9WZW0 |
Ligands and binding sites
- ZN · Zinc ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 131 | 0.49 | 0.79 | 19 | empty |
| 2 | 62 | 0.46 | 0.84 | 16 | empty |
| 3 | 116 | 0.33 | 0.72 | 17 | empty |
| 4 | 58 | 0.30 | 0.75 | 16 | empty |
Interfaces
1 interface between chains.
- B–A · 1499 Ų buried · 46 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 1 disulfide, 1 modified (disulfide, nucleotide modification).
Compared structures
- 2AB4 · Dissecting the Roles of a Strictly Conserved Tyrosine in Substrate Recognition and… · the same entry in another collection · chain B against B, TM-score 1.00
- Q9WZW0 · AlphaFold monomer V2.0 prediction for tRNA pseudouridine synthase B (Q9WZW0) · 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 Q9WZW0
- Elsewhere: RCSB PDB 2AB4 · PDBe 2AB4 · UniProt Q9WZW0
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.