MolNFT v1 · #35390 · protein
Crystal structure of the extracellular domain of kit in complex with stem cell factor (scf)
2E9W · MAST/STEM cell growth factor receptor: “Crystal structure of the extracellular domain of kit in complex with stem cell factor (scf)”. X-ray diffraction, 1 ligand (NAG), 15 pockets (best druggability 0.70). MolNFT v1 #35390 on…
- 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
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