Research workbench
Crystal structure of the catalytic domain of human PUS1 with mes in the active site
Analyse Crystal structure of the catalytic domain of human PUS1 with mes in the active… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4ITS
- Type
- protein
- Length
- 296 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- TRNA pseudouridine synthase a, mitochondrial
- EC
- 5.4.99.12
- UniProt
- Q9Y606
- Ligands
- SO4
- Pockets
- 3 · best druggability 0.57
Structure
x-ray diffraction · 1 distinct chain · 35% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | TRNA pseudouridine synthase a, mitochondrial (EC 5.4.99.12) | protein | 296 | 35% helix, 26% strand | Q9Y606 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 4 copies · chains A
- MES · 2-(N-morpholino)-ethanesulfonic acid · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 118 | 0.57 | 0.84 | 19 | MES, SO4 |
| 2 | 60 | 0.41 | 0.81 | 21 | empty |
| 3 | 62 | 0.29 | 0.74 | 11 | empty |
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 4ITS · Crystal structure of the catalytic domain of human Pus1 with MES in the active site · the same entry in another collection · chain A against A, TM-score 1.00
- Q9Y606 · AlphaFold monomer V2.0 prediction for tRNA pseudouridine synthase a (Q9Y606) · 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 Q9Y606
- Elsewhere: RCSB PDB 4ITS · PDBe 4ITS · UniProt Q9Y606
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