MolNFT v1 · #65914 · protein + RNA
Crystal structure of a substrate-bound full H/ACA rnp from pyrococcus furiosus
3HAY · Probable tRNA pseudouridine synthase B: “Crystal structure of a substrate-bound full H/ACA rnp from pyrococcus furiosus”. X-ray diffraction, 1 ligand (ZN), 9 pockets (best druggability 0.77). MolNFT v1 #65914 on GenesisL1: 3D…
- PDB
- 3HAY
- Type
- protein + RNA
- Length
- 657 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Probable tRNA pseudouridine synthase B; Small nucleolar rnp GAR1-like protein; Ribosome…
- EC
- 5.4.99.-
- UniProt
- Q7LWY0, Q8U029, Q8U1R4, Q8U160
- Ligands
- ZN
- Pockets
- 9 · best druggability 0.77
Structure
x-ray diffraction · 6 distinct chains · 28% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Probable tRNA pseudouridine synthase B (EC 5.4.99.-) | protein | 327 | 28% helix, 31% strand | Q7LWY0 |
| B | Small nucleolar rnp GAR1-like protein | protein | 74 | 0% helix, 51% strand | Q8U029 |
| C | Ribosome biogenesis protein NOP10 | protein | 53 | 23% helix, 15% strand | Q8U1R4 |
| D | 50S ribosomal protein L7AE | protein | 121 | 50% helix, 16% strand | Q8U160 |
| E | H/ACA RNA | rna | 68 | — | — |
| 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
- ZN · Zinc ion · metal · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1079 | 0.77 | 0.79 | 77 | empty |
| 2 | 867 | 0.70 | 0.76 | 35 | empty |
| 3 | 456 | 0.62 | 0.76 | 34 | empty |
| 4 | 260 | 0.51 | 0.75 | 26 | empty |
| 5 | 151 | 0.44 | 0.75 | 26 | empty |
Interfaces
9 interfaces between chains.
- A–E · 1557 Ų buried · 23 hydrogen bonds · protein-nucleic
- A–C · 1426 Ų buried · 19 hydrogen bonds · protein-protein
- A–F · 984 Ų buried · 26 hydrogen bonds · protein-nucleic
- E–F · 763 Ų buried · 44 hydrogen bonds · nucleic-nucleic
- C–D · 747 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 modified (nucleotide modification).
Compared structures
- 3HAY · Crystal structure of a substrate-bound full 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 0.98
- 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 0.93
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 Q8U029
- Every structure of UniProt Q8U1R4
- Every structure of UniProt Q8U160
- Elsewhere: RCSB PDB 3HAY · PDBe 3HAY · UniProt Q7LWY0 · UniProt Q8U029 · UniProt Q8U1R4 · UniProt Q8U160
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