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Crystal structure of S. cerevisiae HBS1 protein (GDP-bound form), a translational GTPase involved in RNA quality control pathways and interacting with DOM34/PELOTA
Analyse Crystal structure of S. cerevisiae HBS1 protein (GDP-bound form), a… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3P27
- Type
- protein
- Length
- 877 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Elongation factor 1 alpha-like protein
- UniProt
- P32769
- Ligands
- GDP
- Pockets
- 12 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 22% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Elongation factor 1 alpha-like protein | protein | 433 | 22% helix, 33% strand | P32769 |
| B | Elongation factor 1 alpha-like protein | protein | 444 | 22% helix, 33% strand | P32769 |
Ligands and binding sites
- GDP · Guanosine-5'-diphosphate · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 719 | 0.76 | 0.81 | 85 | empty |
| 2 | 70 | 0.74 | 0.98 | 21 | empty |
| 3 | 67 | 0.74 | 0.98 | 22 | empty |
| 4 | 625 | 0.73 | 0.80 | 71 | empty |
| 5 | 378 | 0.72 | 0.84 | 56 | empty |
Interfaces
1 interface between chains.
- A–B · 1593 Ų buried · 24 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 18 modified (engineered).
Compared structures
- 3P27 · Crystal structure of S. cerevisiae Hbs1 protein (GDP-bound form), a translational GTPase… · the same entry in another collection · chain A against A, TM-score 1.00
- P32769 · AlphaFold monomer V2.0 prediction for elongation factor 1 alpha-like protein (P32769) · a predicted model of the same protein · chain A against A, TM-score 0.97
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 P32769
- Elsewhere: RCSB PDB 3P27 · PDBe 3P27 · UniProt P32769
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