Research workbench
Crystal structure of a substrate-bound GAR1-minus H/ACA rnp from pyrococcus furiosus
Analyse Crystal structure of a substrate-bound GAR1-minus H/ACA rnp from pyrococcus… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3HAX
- Type
- protein + RNA
- Length
- 575 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Probable tRNA pseudouridine synthase B; Ribosome biogenesis protein NOP10; 50S ribosomal…
- EC
- 5.4.99.-
- UniProt
- Q7LWY0, Q8U1R4, Q8U160
- Ligands
- MG, ZN
- Pockets
- 7 · best druggability 0.80
Structure
x-ray diffraction · 5 distinct chains · 33% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Probable tRNA pseudouridine synthase B (EC 5.4.99.-) | protein | 329 | 27% helix, 32% strand | Q7LWY0 |
| C | Ribosome biogenesis protein NOP10 | protein | 53 | 23% helix, 15% strand | Q8U1R4 |
| D | 50S ribosomal protein L7AE | protein | 121 | 51% helix, 16% strand | Q8U160 |
| E | H/ACA RNA | rna | 58 | — | — |
| F | 5'-R(*AP*UP*AP*AP*UP*UP*(FHU)P*GP*AP*CP*UP*CP*AP*A)-3' | rna | 14 | — | — |
Ligands and binding sites
- MG · Magnesium ion · metal · 5 copies · chains E
- ZN · Zinc ion · metal · chains C
- PGE · Triethylene glycol · additive · 2 copies · chains A
- EDO · 1,2-ethanediol · additive · 2 copies · chains A, D
- PG4 · Tetraethylene glycol · additive · chains A, C, D, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 806 | 0.80 | 0.84 | 67 | PG4, MG |
| 2 | 848 | 0.69 | 0.76 | 35 | MG |
| 3 | 467 | 0.63 | 0.77 | 32 | empty |
| 4 | 230 | 0.50 | 0.75 | 35 | empty |
| 5 | 92 | 0.42 | 0.78 | 16 | empty |
Interfaces
8 interfaces between chains.
- A–E · 1657 Ų buried · 38 hydrogen bonds · protein-nucleic
- A–C · 1427 Ų buried · 26 hydrogen bonds · protein-protein
- A–F · 971 Ų buried · 29 hydrogen bonds · protein-nucleic
- E–F · 752 Ų buried · 57 hydrogen bonds · nucleic-nucleic
- C–D · 677 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 modified (nucleotide modification).
Compared structures
- 3HAX · Crystal structure of a substrate-bound Gar1-minus H/ACA RNP from Pyrococcus furiosus · the same entry in another collection · chain F against F, TM-score 1.00
- Q8U160 · AlphaFold monomer V2.0 prediction for 50S ribosomal protein L7AE (Q8U160) · a predicted model of the same protein · chain D 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 C against A, TM-score 0.92
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 3HAX · PDBe 3HAX · UniProt Q7LWY0 · UniProt Q8U1R4 · UniProt Q8U160
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