Research workbench
Steroid receptor RNA activator (sra) modification by the human pseudouridine synthase 1 (HPUS1P): RNA binding, activity, and atomic model
Analyse Steroid receptor RNA activator (sra) modification by the human pseudouridine… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4NZ6
- Type
- protein
- Length
- 614 residues
- Chains
- 2
- 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
- DLY, DGL
- Pockets
- 6 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 35% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | TRNA pseudouridine synthase a, mitochondrial (EC 5.4.99.12) | protein | 305 | 35% helix, 23% strand | Q9Y606 |
| B | TRNA pseudouridine synthase a, mitochondrial (EC 5.4.99.12) | protein | 309 | 35% helix, 24% strand | Q9Y606 |
Ligands and binding sites
- DLY · D-lysine · ligand · chains A
- DGL · D-glutamic acid · ligand · chains B
- EDO · 1,2-ethanediol · additive · chains A
- PGE · Triethylene glycol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1134 | 0.77 | 0.79 | 102 | DLY |
| 2 | 191 | 0.60 | 0.82 | 27 | DGL |
| 3 | 74 | 0.50 | 0.84 | 20 | empty |
| 4 | 76 | 0.40 | 0.79 | 22 | empty |
| 5 | 57 | 0.29 | 0.74 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 393 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 4NZ6 · Steroid receptor RNA Activator (SRA) modification by the human Pseudouridine Synthase 1… · 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 0.99
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 Q9Y606
- Elsewhere: RCSB PDB 4NZ6 · PDBe 4NZ6 · UniProt Q9Y606
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