Research workbench
Crystal structure of pseudouridine synthase rlua: indirect sequence readout through protein-induced RNA structure
Analyse Crystal structure of pseudouridine synthase rlua: indirect sequence readout… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2I82
- Type
- protein + RNA
- Length
- 946 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5'- R(*GP*AP*GP*GP*GP*GP*AP*UP*UP*GP*AP*AP*AP*AP*UP*CP*CP*CP*CP *UP*C)-3'; Ribosomal…
- EC
- 4.2.1.70
- UniProt
- P0AA37
- Ligands
- FOU
- Pockets
- 10 · best druggability 0.72
Structure
x-ray diffraction · 5 distinct chains · 17% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| E, F, G, H | 5'- R(*GP*AP*GP*GP*GP*GP*AP*UP*UP*GP*AP*AP*AP*AP*UP*CP*CP*CP*CP *UP*C)-3' | rna | 21 | — | — |
| A | Ribosomal large subunit pseudouridine synthase a (EC 4.2.1.70) | protein | 217 | 18% helix, 35% strand | P0AA37 |
| B | Ribosomal large subunit pseudouridine synthase a (EC 4.2.1.70) | protein | 214 | 17% helix, 34% strand | P0AA37 |
| C | Ribosomal large subunit pseudouridine synthase a (EC 4.2.1.70) | protein | 215 | 18% helix, 34% strand | P0AA37 |
| D | Ribosomal large subunit pseudouridine synthase a (EC 4.2.1.70) | protein | 216 | 17% helix, 35% strand | P0AA37 |
Ligands and binding sites
- FOU · (5S,6R)-5-fluoro-6-hydroxydihydropyrimidine-2,4(1H,3H)-dione · ligand · 2 copies · chains E, A, G, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 527 | 0.72 | 0.81 | 28 | empty |
| 2 | 512 | 0.70 | 0.80 | 28 | empty |
| 3 | 367 | 0.69 | 0.83 | 25 | empty |
| 4 | 593 | 0.67 | 0.78 | 27 | empty |
| 5 | 98 | 0.43 | 0.79 | 16 | empty |
Interfaces
8 interfaces between chains.
- E–A · 1532 Ų buried · 45 hydrogen bonds · protein-nucleic
- F–B · 1475 Ų buried · 37 hydrogen bonds · protein-nucleic
- G–C · 1464 Ų buried · 38 hydrogen bonds · protein-nucleic
- H–D · 1339 Ų buried · 42 hydrogen bonds · protein-nucleic
- A–C · 508 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 29 modified, 2 covalent (engineered, covalent ligand).
Compared structures
- 2I82 · Crystal structure of pseudouridine synthase RluA: indirect sequence readout through… · the same entry in another collection · chain D against D, TM-score 1.00
- P0AA37 · AlphaFold monomer V2.0 prediction for dual-specificity RNA pseudouridine synthase rlua… · 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 P0AA37
- Elsewhere: RCSB PDB 2I82 · PDBe 2I82 · UniProt P0AA37
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