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
- 2QJ2
- Type
- protein
- Length
- 349 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hepatocyte growth factor
- UniProt
- P14210
- Ligands
- SO4
- Pockets
- 5 · best druggability 0.73
Structure
x-ray diffraction · 2 distinct chains · 11% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hepatocyte growth factor | protein | 174 | 11% helix, 28% strand | P14210 |
| B | Hepatocyte growth factor | protein | 175 | 11% helix, 31% strand | P14210 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 4 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 614 | 0.73 | 0.80 | 65 | empty |
| 2 | 53 | 0.53 | 0.88 | 17 | empty |
| 3 | 84 | 0.46 | 0.81 | 20 | empty |
| 4 | 101 | 0.37 | 0.75 | 24 | empty |
| 5 | 83 | 0.34 | 0.74 | 15 | SO4 |
Interfaces
1 interface between chains.
- A–B · 1342 Ų buried · 21 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 disulfide (disulfide).
Compared structures
- 2QJ2 · 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
- P14210 · AlphaFold monomer V2.0 prediction for hepatocyte growth factor (P14210) · a predicted model of the same protein · chain B against A, TM-score 0.59
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 P14210
- Elsewhere: RCSB PDB 2QJ2 · PDBe 2QJ2 · UniProt P14210
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