Research workbench
Crystal structure of the extracellular domain of kit in complex with stem cell factor (scf)
Analyse Crystal structure of the extracellular domain of kit in complex with stem cell… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2E9W
- Type
- protein
- Length
- 1,197 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- MAST/STEM cell growth factor receptor; Kit ligand
- EC
- 2.7.10.1
- UniProt
- P10721, P21583
- Ligands
- NAG
- Pockets
- 15 · best druggability 0.70
Structure
x-ray diffraction · 4 distinct chains · 12% helix, 39% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | MAST/STEM cell growth factor receptor (EC 2.7.10.1) | protein | 468 | 2% helix, 48% strand | P10721 |
| B | MAST/STEM cell growth factor receptor (EC 2.7.10.1) | protein | 469 | 1% helix, 48% strand | P10721 |
| C | Kit ligand | protein | 132 | 51% helix, 5% strand | P21583 |
| D | Kit ligand | protein | 128 | 48% helix, 5% strand | P21583 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 6 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 133 | 0.70 | 0.91 | 27 | empty |
| 2 | 151 | 0.68 | 0.89 | 27 | empty |
| 3 | 612 | 0.65 | 0.75 | 61 | empty |
| 4 | 425 | 0.63 | 0.77 | 57 | empty |
| 5 | 130 | 0.47 | 0.78 | 21 | empty |
Interfaces
4 interfaces between chains.
- B–D · 935 Ų buried · 19 hydrogen bonds · protein-protein
- A–C · 934 Ų buried · 17 hydrogen bonds · protein-protein
- C–D · 771 Ų buried · 13 hydrogen bonds · protein-protein
- A–B · 243 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 13 disulfide, 6 glycan (disulfide, N-glycosylation).
Compared structures
- 2E9W · Crystal structure of the extracellular domain of Kit in complex with stem cell factor… · the same entry in another collection · chain D against D, TM-score 1.00
- P10721 · AlphaFold monomer V2.0 prediction for MAST/STEM cell growth factor receptor kit (P10721) · a predicted model of the same protein · chain B against A, TM-score 0.95
- P21583 · AlphaFold monomer V2.0 prediction for kit ligand (P21583) · a predicted model of the same protein · chain D against A, TM-score 0.87
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 P10721
- Every structure of UniProt P21583
- Elsewhere: RCSB PDB 2E9W · PDBe 2E9W · UniProt P10721 · UniProt P21583
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.