Research workbench
Crystal structure of sulfolobus solfataricus peptidyl-tRNA hydrolase
Analyse Crystal structure of sulfolobus solfataricus peptidyl-tRNA hydrolase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1XTY
- Type
- protein
- Length
- 480 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Peptidyl-tRNA hydrolase
- EC
- 3.1.1.29
- UniProt
- Q980V1
- Ligands
- SO4
- Pockets
- 5 · best druggability 0.50
Structure
x-ray diffraction · 1 distinct chain · 44% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Peptidyl-tRNA hydrolase (EC 3.1.1.29) | protein | 120 | 44% helix, 26% strand | Q980V1 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 8 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 180 | 0.50 | 0.77 | 21 | SO4 |
| 2 | 179 | 0.50 | 0.77 | 21 | SO4 |
| 3 | 182 | 0.49 | 0.76 | 26 | SO4 |
| 4 | 189 | 0.46 | 0.74 | 23 | empty |
| 5 | 160 | 0.45 | 0.75 | 21 | SO4 |
Interfaces
4 interfaces between chains.
- A–B · 910 Ų buried · 4 hydrogen bonds · protein-protein
- C–D · 901 Ų buried · 3 hydrogen bonds · protein-protein
- B–D · 237 Ų buried · 1 hydrogen bond · protein-protein
- A–C · 30 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 1XTY · Crystal structure of Sulfolobus solfataricus peptidyl-tRNA hydrolase · the same entry in another collection · chain A against A, TM-score 1.00
- Q980V1 · AlphaFold monomer V2.0 prediction for peptidyl-tRNA hydrolase (Q980V1) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 Q980V1
- Elsewhere: RCSB PDB 1XTY · PDBe 1XTY · UniProt Q980V1
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