Research workbench
A mechanistic basis for converting a receptor tyrosine kinase agonist to an antagonist
Analyse A mechanistic basis for converting a receptor tyrosine kinase agonist to an… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2QJ4
- Type
- protein
- Length
- 344 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hepatocyte growth factor
- UniProt
- Q08048
- Ligands
- SO4
- Pockets
- 5 · best druggability 0.70
Structure
x-ray diffraction · 1 distinct chain · 8% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Hepatocyte growth factor | protein | 172 | 8% helix, 30% strand | Q08048 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 499 | 0.70 | 0.80 | 62 | empty |
| 2 | 254 | 0.54 | 0.77 | 48 | empty |
| 3 | 232 | 0.53 | 0.77 | 32 | empty |
| 4 | 64 | 0.29 | 0.74 | 15 | empty |
| 5 | 53 | 0.26 | 0.74 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 1231 Ų buried · 18 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 disulfide (disulfide).
Compared structures
- 2QJ4 · A Mechanistic Basis for Converting a Receptor Tyrosine Kinase Agonist to an Antagonist · the same entry in another collection · chain A against A, TM-score 1.00
- Q08048 · AlphaFold monomer V2.0 prediction for hepatocyte growth factor (Q08048) · a predicted model of the same protein · chain A against A, TM-score 0.60
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 Q08048
- Elsewhere: RCSB PDB 2QJ4 · PDBe 2QJ4 · UniProt Q08048
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