4K9E
Crystal structure of KIT D4D5 fragment in complex with anti-Kit antibodies Fab79D
- PDB DOI: https://doi.org/10.2210/pdb4K9E/pdb
- Classification: IMMUNE SYSTEM
- Organism(s): Mus musculus, Homo sapiens
- Expression System: Escherichia coli, unidentified baculovirus
- Mutation(s): No
- Deposited: 2013-04-19 Released: 2013-10-16
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.70 Å
- R-Value Free: 0.282
- R-Value Work: 0.247
- R-Value Observed: 0.248
This is version 1.2 of the entry. See complete history.
Macromolecules
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 1 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| light chain | A [auth L] | 228 | Mus musculus | Mutation(s): 0 |  |
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
Sequence AnnotationsExpand | |||||
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Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 2 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| heavy chain | B [auth H] | 221 | Mus musculus | Mutation(s): 0 |  |
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
Sequence AnnotationsExpand | |||||
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Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 3 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Mast/stem cell growth factor receptor Kit | 214 | Homo sapiens | Mutation(s): 0 Gene Names: KIT, SCFR EC: 2.7.10.1 |  | |
UniProt & NIH Common Fund Data Resources | |||||
Find proteins for P10721 (Homo sapiens) Explore P10721 Go to UniProtKB: P10721 | |||||
PHAROS: P10721 GTEx: ENSG00000157404 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | P10721 | ||||
Sequence AnnotationsExpand | |||||
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Small Molecules
| Ligands 1 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| NAG Query on NAG | D [auth C] | 2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N |  | ||
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.70 Å
- R-Value Free: 0.282
- R-Value Work: 0.247
- R-Value Observed: 0.248
- Space Group: P 65 2 2
- Diffraction Data: https://doi.org/10.15785/SBGRID/163
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 94.577 | α = 90 |
| b = 94.577 | β = 90 |
| c = 320.876 | γ = 120 |
| Software Name | Purpose |
|---|---|
| DENZO | data reduction |
| SCALEPACK | data scaling |
| PHASER | phasing |
| PHENIX | refinement |
| PDB_EXTRACT | data extraction |
| CBASS | data collection |
Entry History
Deposition Data
- Released Date: 2013-10-16 Deposition Author(s): Resheynyak, A.V., Boggon, T.J., Lax, I., Schlessinger, J.
Revision History (Full details and data files)
- Version 1.0: 2013-10-16
Type: Initial release - Version 1.1: 2014-03-12
Changes: Database references - Version 1.2: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Data collection, Database references, Derived calculations, Structure summary
