6KX1
Crystal structure of SN-101 mAb in complex with MUC1 glycopeptide
- PDB DOI: https://doi.org/10.2210/pdb6KX1/pdb
- Classification: IMMUNE SYSTEM
- Organism(s): Mus musculus, Homo sapiens
- Expression System: Mus musculus
- Mutation(s): No
- Deposited: 2019-09-09 Released: 2020-07-29
- Funding Organization(s): Japan Society for the Promotion of Science
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.77 Å
- R-Value Free: 0.229
- R-Value Work: 0.177
- R-Value Observed: 0.179
This is version 1.1 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 |
| Fab Fragment-SN-101-Heavy chain | 236 | 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 |
| Fab Fragment-SN-101-Light chain | 239 | 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: Sequence | 3D Structure
Entity ID: 3 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Synthetic MUC1 glycopepide | 16 | Homo sapiens | Mutation(s): 0 |  | |
UniProt & NIH Common Fund Data Resources | |||||
Find proteins for P15941 (Homo sapiens) Explore P15941 Go to UniProtKB: P15941 | |||||
PHAROS: P15941 GTEx: ENSG00000185499 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | P15941 | ||||
Sequence AnnotationsExpand | |||||
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Small Molecules
| Ligands 1 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| A2G (Subject of Investigation/LOI) Query on A2G | D [auth C] | 2-acetamido-2-deoxy-alpha-D-galactopyranose C8 H15 N O6 OVRNDRQMDRJTHS-CBQIKETKSA-N |  | ||
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 1.77 Å
- R-Value Free: 0.229
- R-Value Work: 0.177
- R-Value Observed: 0.179
- Space Group: C 1 2 1
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 159.92 | α = 90 |
| b = 39.98 | β = 100.56 |
| c = 63.87 | γ = 90 |
| Software Name | Purpose |
|---|---|
| PHENIX | refinement |
| XDS | data reduction |
| XDS | data scaling |
| PHASER | phasing |
Entry History & Funding Information
Deposition Data
- Released Date: 2020-07-29 Deposition Author(s): Wakui, H., Tanaka, Y., Kato, K., Ose, T., Matsumoto, I., Min, Y., Tachibana, T., Nishimura, S.-I.
| Funding Organization | Location | Grant Number |
|---|---|---|
| Japan Society for the Promotion of Science | Japan | 25220206 |
| Japan Society for the Promotion of Science | Japan | 19H00918 |
Revision History (Full details and data files)
- Version 1.0: 2020-07-29
Type: Initial release - Version 1.1: 2023-11-22
Changes: Data collection, Database references, Refinement description, Structure summary
