Research workbench
Crystal structure of kit D4D5 fragment in complex with anti-kit antibodies FAB79D
Analyse Crystal structure of kit D4D5 fragment in complex with anti-kit antibodies… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4K9E
- Type
- protein
- Length
- 634 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Light chain; Heavy chain; MAST/STEM cell growth factor receptor kit
- EC
- 2.7.10.1
- UniProt
- P10721
- Ligands
- NAG
- Pockets
- 7 · best druggability 0.59
Structure
x-ray diffraction · 3 distinct chains · 4% helix, 54% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L | Light chain | protein | 221 | 7% helix, 51% strand | — |
| H | Heavy chain | protein | 220 | 4% helix, 52% strand | — |
| C | MAST/STEM cell growth factor receptor kit (EC 2.7.10.1) | protein | 193 | 2% helix, 59% strand | P10721 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains H, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 80 | 0.59 | 0.88 | 21 | empty |
| 2 | 437 | 0.58 | 0.74 | 43 | empty |
| 3 | 50 | 0.50 | 0.88 | 20 | empty |
| 4 | 149 | 0.46 | 0.76 | 25 | empty |
| 5 | 122 | 0.41 | 0.75 | 25 | empty |
Interfaces
3 interfaces between chains.
- L–H · 1837 Ų buried · 12 hydrogen bonds · protein-protein
- H–C · 890 Ų buried · 12 hydrogen bonds · protein-protein
- L–C · 353 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
- 4K9E · Crystal structure of KIT D4D5 fragment in complex with anti-Kit antibodies Fab79D · the same entry in another collection · chain L against L, 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 C against A, TM-score 0.84
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
- Elsewhere: RCSB PDB 4K9E · PDBe 4K9E · UniProt P10721
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