MolNFT v1 · #62937 · protein
Structure of the cs domain of the essential H/ACA rnp assembly protein SHQ1P
3EUD: “Structure of the cs domain of the essential H/ACA rnp assembly protein SHQ1P”. X-ray diffraction, 9 pockets (best druggability 0.48). MolNFT v1 #62937 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 3EUD
- Type
- protein
- Length
- 577 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein SHQ1
- UniProt
- P40486
- Pockets
- 9 · best druggability 0.48
Structure
x-ray diffraction · 3 distinct chains · 3% helix, 47% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protein SHQ1 | protein | 99 | 4% helix, 46% strand | P40486 |
| B, C, E | Protein SHQ1 | protein | 98 | 4% helix, 46% strand | P40486 |
| D, F | Protein SHQ1 | protein | 92 | 0% helix, 49% strand | P40486 |
Pockets
9 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 122 | 0.48 | 0.79 | 18 | empty |
| 2 | 135 | 0.44 | 0.76 | 34 | empty |
| 3 | 102 | 0.44 | 0.79 | 22 | empty |
| 4 | 103 | 0.43 | 0.78 | 16 | empty |
| 5 | 77 | 0.40 | 0.79 | 23 | empty |
Interfaces
7 interfaces between chains.
- D–F · 854 Ų buried · 9 hydrogen bonds · protein-protein
- C–D · 655 Ų buried · 8 hydrogen bonds · protein-protein
- B–F · 563 Ų buried · 8 hydrogen bonds · protein-protein
- A–D · 557 Ų buried · 11 hydrogen bonds · protein-protein
- E–F · 532 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 modified (engineered).
Compared structures
- 3EUD · Structure of the CS domain of the essential H/ACA RNP assembly protein Shq1p · the same entry in another collection · chain F against F, TM-score 1.00
- P40486 · AlphaFold monomer V2.0 prediction for protein SHQ1 (P40486) · a predicted model of the same protein · chain A against A, TM-score 0.95
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 P40486
- Elsewhere: RCSB PDB 3EUD · PDBe 3EUD · UniProt P40486
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