Research workbench
Structural basis of neurohormone perception by the receptor tyrosine kinase torso
Analyse Structural basis of neurohormone perception by the receptor tyrosine kinase… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5AOQ
- Type
- protein
- Length
- 640 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Torso; Preproptth
- EC
- 2.7.10.1
- UniProt
- D2IYS2, Q17238
- Ligands
- NAG
- Pockets
- 10 · best druggability 0.86
Structure
x-ray diffraction · 3 distinct chains · 7% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Torso (EC 2.7.10.1) | protein | 233 | 10% helix, 44% strand | D2IYS2 |
| L | Preproptth | protein | 86 | 0% helix, 41% strand | Q17238 |
| M | Preproptth | protein | 88 | 3% helix, 38% strand | Q17238 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1103 | 0.86 | 0.86 | 115 | empty |
| 2 | 55 | 0.67 | 0.96 | 16 | empty |
| 3 | 241 | 0.55 | 0.78 | 31 | empty |
| 4 | 215 | 0.54 | 0.78 | 32 | empty |
| 5 | 167 | 0.52 | 0.79 | 34 | empty |
Interfaces
6 interfaces between chains.
- L–M · 1361 Ų buried · 12 hydrogen bonds · protein-protein
- B–L · 934 Ų buried · 8 hydrogen bonds · protein-protein
- A–B · 880 Ų buried · 10 hydrogen bonds · protein-protein
- A–M · 774 Ų buried · 6 hydrogen bonds · protein-protein
- B–M · 593 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 15 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 5AOQ · Structural basis of neurohormone perception by the receptor tyrosine kinase Torso · the same entry in another collection · chain A against A, TM-score 1.00
- D2IYS2 · AlphaFold monomer V2.0 prediction for tyrosine-protein kinase receptor torso (D2IYS2) · a predicted model of the same protein · chain A against A, TM-score 0.88
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 D2IYS2
- Every structure of UniProt Q17238
- Elsewhere: RCSB PDB 5AOQ · PDBe 5AOQ · UniProt D2IYS2 · UniProt Q17238
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