Research workbench
Crystal structure of the archaeal box H/ACA srnp NOP10-CBF5 complex
Analyse Crystal structure of the archaeal box H/ACA srnp NOP10-CBF5 complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2AUS
- Type
- protein
- Length
- 726 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pseudouridine synthase; Ribosome biogenesis protein NOP10
- EC
- 5.4.99.-
- UniProt
- Q9V1A5, Q9V0E3
- Ligands
- ZN, PO4
- Pockets
- 7 · best druggability 0.52
Structure
x-ray diffraction · 3 distinct chains · 29% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C | Pseudouridine synthase (EC 5.4.99.-) | protein | 311 | 30% helix, 33% strand | Q9V1A5 |
| D, B | Ribosome biogenesis protein NOP10 | protein | 53 | 21% helix, 15% strand | Q9V0E3 |
| A | Pseudouridine synthase (EC 5.4.99.-) | protein | 309 | 29% helix, 33% strand | Q9V1A5 |
Ligands and binding sites
- ZN · Zinc ion · metal · 2 copies · chains D, B
- PO4 · Phosphate ion · ion · 5 copies · chains C, D, A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 251 | 0.52 | 0.75 | 35 | empty |
| 2 | 110 | 0.42 | 0.77 | 23 | empty |
| 3 | 102 | 0.42 | 0.77 | 19 | PO4 |
| 4 | 83 | 0.42 | 0.79 | 22 | PO4 |
| 5 | 131 | 0.41 | 0.75 | 13 | empty |
Interfaces
4 interfaces between chains.
- A–B · 1379 Ų buried · 23 hydrogen bonds · protein-protein
- C–D · 1318 Ų buried · 21 hydrogen bonds · protein-protein
- C–A · 582 Ų buried · 7 hydrogen bonds · protein-protein
- D–A · 75 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 2AUS · Crystal structure of the archaeal box H/ACA sRNP Nop10-Cbf5 complex · the same entry in another collection · chain C against C, TM-score 1.00
- Q9V1A5 · AlphaFold monomer V2.0 prediction for probable tRNA pseudouridine synthase B (Q9V1A5) · a predicted model of the same protein · chain A against A, TM-score 0.98
- Q9V0E3 · AlphaFold monomer V2.0 prediction for ribosome biogenesis protein NOP10 (Q9V0E3) · a predicted model of the same protein · chain D against A, TM-score 0.83
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 Q9V1A5
- Every structure of UniProt Q9V0E3
- Elsewhere: RCSB PDB 2AUS · PDBe 2AUS · UniProt Q9V1A5 · UniProt Q9V0E3
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.