Research workbench
Structure of a functional ribonucleoprotein pseudouridine synthase bound to a substrate RNA
Analyse Structure of a functional ribonucleoprotein pseudouridine synthase bound to a… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3HJW
- Type
- protein + RNA
- Length
- 571 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pseudouridine synthase CBF5; Ribosome biogenesis protein NOP10; 50S ribosomal protein…
- EC
- 5.4.99.-
- UniProt
- Q7LWY0, Q8U1R4, Q8U160
- Ligands
- ZN, K
- Pockets
- 8 · best druggability 0.80
Structure
x-ray diffraction · 5 distinct chains · 33% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Pseudouridine synthase CBF5 (EC 5.4.99.-) | protein | 327 | 28% helix, 33% strand | Q7LWY0 |
| B | Ribosome biogenesis protein NOP10 | protein | 53 | 23% helix, 15% strand | Q8U1R4 |
| C | 50S ribosomal protein L7AE | protein | 120 | 49% helix, 16% strand | Q8U160 |
| D | RNA (58-mer) | rna | 58 | — | — |
| E | 5'-R(*GP*AP*GP*CP*GP*(FHU)P*GP*CP*GP*GP*UP*UP*U)-3' | rna | 13 | — | — |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 644 | 0.80 | 0.85 | 52 | empty |
| 2 | 586 | 0.69 | 0.79 | 35 | empty |
| 3 | 447 | 0.62 | 0.76 | 34 | empty |
| 4 | 144 | 0.42 | 0.74 | 22 | empty |
| 5 | 106 | 0.41 | 0.77 | 18 | empty |
Interfaces
8 interfaces between chains.
- A–D · 1609 Ų buried · 38 hydrogen bonds · protein-nucleic
- A–B · 1482 Ų buried · 29 hydrogen bonds · protein-protein
- A–E · 988 Ų buried · 25 hydrogen bonds · protein-nucleic
- D–E · 700 Ų buried · 64 hydrogen bonds · nucleic-nucleic
- C–D · 696 Ų buried · 22 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 4 disulfide, 1 modified (disulfide, nucleotide modification).
Compared structures
- 3HJW · Structure of a functional ribonucleoprotein pseudouridine synthase bound to a substrate… · the same entry in another collection · chain E against E, TM-score 1.00
- Q8U160 · AlphaFold monomer V2.0 prediction for 50S ribosomal protein L7AE (Q8U160) · a predicted model of the same protein · chain C against A, TM-score 0.99
- Q7LWY0 · AlphaFold monomer V2.0 prediction for probable tRNA pseudouridine synthase B (Q7LWY0) · a predicted model of the same protein · chain A against A, TM-score 0.98
- Q8U1R4 · AlphaFold monomer V2.0 prediction for ribosome biogenesis protein NOP10 (Q8U1R4) · a predicted model of the same protein · chain B against A, TM-score 0.93
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 Q7LWY0
- Every structure of UniProt Q8U1R4
- Every structure of UniProt Q8U160
- Elsewhere: RCSB PDB 3HJW · PDBe 3HJW · UniProt Q7LWY0 · UniProt Q8U1R4 · UniProt Q8U160
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