5N7B
Understanding the singular conformational landscape of the Tn antigens: Sulfur-for- oxygen substitution in the glycosidic linkage provides new insights into molecular recognition by an antibody
- PDB DOI: https://doi.org/10.2210/pdb5N7B/pdb
- Classification: IMMUNE SYSTEM
- Organism(s): Mus musculus, synthetic construct
- Expression System: Komagataella phaffii GS115
- Mutation(s): No
- Deposited: 2017-02-20 Released: 2018-06-27
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.70 Å
- R-Value Free: 0.211
- R-Value Work: 0.176
- R-Value Observed: 0.177
This is version 2.1 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 |
| Ig heavy chain V-III region J606,Ig lambda-1 chain V region S43 | A [auth H] | 244 | Mus musculus | Mutation(s): 0 |  |
UniProt | |||||
Find proteins for P01727 (Mus musculus) Explore P01727 Go to UniProtKB: P01727 | |||||
Find proteins for P01801 (Mus musculus) Explore P01801 Go to UniProtKB: P01801 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Groups | P01801P01727 | ||||
Sequence AnnotationsExpand | |||||
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Find similar proteins by: Sequence | 3D Structure
Entity ID: 2 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| APD(CG6)RP(NH2) peptide | B [auth I] | 7 | synthetic construct | Mutation(s): 0 |  |
Sequence AnnotationsExpand | |||||
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Small Molecules
| Ligands 2 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| A2G Query on A2G | J [auth I] | 2-acetamido-2-deoxy-alpha-D-galactopyranose C8 H15 N O6 OVRNDRQMDRJTHS-CBQIKETKSA-N |  | ||
| EDO Query on EDO | C [auth H] D [auth H] E [auth H] F [auth H] G [auth H] | 1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N |  | ||
| Modified Residues 1 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Type | Formula | 2D Diagram | Parent |
| CG6 Query on CG6 | B [auth I] | L-PEPTIDE LINKING | C4 H9 N O2 S |  | CYS |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 1.70 Å
- R-Value Free: 0.211
- R-Value Work: 0.176
- R-Value Observed: 0.177
- Space Group: P 21 21 21
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 35.403 | α = 90 |
| b = 68.648 | β = 90 |
| c = 90.917 | γ = 90 |
| Software Name | Purpose |
|---|---|
| REFMAC | refinement |
| XDS | data reduction |
| SCALA | data scaling |
| MOLREP | phasing |
Entry History & Funding Information
Deposition Data
- Released Date: 2018-06-27 Deposition Author(s): Companon, I., Martinez-Saez, N., Castro-Lopez, J., Jimenez-Barbero, J., Bernardes, G.J.L., Busto, J.H., Avenoza, A., Jimenez-Oses, G., Hurtado-Guerrero, R., Peregrina, J.M., Corzana, F.
| Funding Organization | Location | Grant Number |
|---|---|---|
| Spain | -- |
Revision History (Full details and data files)
- Version 1.0: 2018-06-27
Type: Initial release - Version 1.1: 2019-07-10
Changes: Data collection, Database references - Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Data collection, Derived calculations, Structure summary - Version 2.1: 2024-01-17
Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary
