Research workbench
Structure of a class III rtk signaling assembly
Analyse Structure of a class III rtk signaling assembly in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2O26
- Type
- protein
- Length
- 1,661 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Kit ligand; MAST/STEM cell growth factor receptor
- EC
- 2.7.10.1
- UniProt
- P20826, P05532
- Ligands
- NAG, FUL, MAN
- Pockets
- 12 · best druggability 0.77
Structure
x-ray diffraction · 3 distinct chains · 25% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Kit ligand | protein | 144 | 46% helix, 7% strand | P20826 |
| B, E, F | Kit ligand | protein | 139 | 47% helix, 7% strand | P20826 |
| X, Y, U, W | MAST/STEM cell growth factor receptor (EC 2.7.10.1) | protein | 275 | 2% helix, 52% strand | P05532 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 16 copies · chains X, Y, U, W
- FUL · beta-L-fucopyranose · sugar · 4 copies · chains X, Y, U, W
- MAN · alpha-D-mannopyranose · sugar · 4 copies
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1145 | 0.77 | 0.79 | 124 | empty |
| 2 | 982 | 0.76 | 0.79 | 102 | empty |
| 3 | 890 | 0.75 | 0.78 | 100 | empty |
| 4 | 811 | 0.74 | 0.78 | 94 | empty |
| 5 | 174 | 0.67 | 0.87 | 33 | empty |
Interfaces
7 interfaces between chains.
- E–U · 1382 Ų buried · 19 hydrogen bonds · protein-protein
- B–Y · 1320 Ų buried · 14 hydrogen bonds · protein-protein
- A–X · 1297 Ų buried · 17 hydrogen bonds · protein-protein
- F–W · 1259 Ų buried · 15 hydrogen bonds · protein-protein
- E–F · 753 Ų buried · 20 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 24 disulfide, 8 glycan (disulfide, N-glycosylation).
Compared structures
- 2O26 · Structure of a class III RTK signaling assembly · the same entry in another collection · chain W against W, TM-score 1.00
- P05532 · AlphaFold monomer V2.0 prediction for MAST/STEM cell growth factor receptor kit (P05532) · a predicted model of the same protein · chain X against A, TM-score 0.96
- P20826 · AlphaFold monomer V2.0 prediction for kit ligand (P20826) · a predicted model of the same protein · chain B against A, TM-score 0.89
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 P20826
- Every structure of UniProt P05532
- Elsewhere: RCSB PDB 2O26 · PDBe 2O26 · UniProt P20826 · UniProt P05532
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.