6CX7
Structure of alpha-GSA[12,6P] bound by CD1d and in complex with the Va14Vb8.2 TCR
- PDB DOI: https://doi.org/10.2210/pdb6CX7/pdb
- Classification: IMMUNE SYSTEM
- Organism(s): Mus musculus
- Expression System: Spodoptera frugiperda, Escherichia coli 'BL21-Gold(DE3)pLysS AG
- Mutation(s): No 
- Deposited: 2018-04-02 Released: 2019-04-10 
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.60 Å
- R-Value Free: 0.239 
- R-Value Work: 0.208 
- R-Value Observed: 0.209 
This is version 2.1 of the entry. See complete history. 
Macromolecules
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 1 | |||||
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Molecule | Chains | Sequence Length | Organism | Details | Image |
Chimeric T cell antigen receptor alpha chain Va14,Va24,Ja18 | A [auth C] | 209 | 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 | |||||
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Molecule | Chains | Sequence Length | Organism | Details | Image |
Chimeric T cell antigen receptor beta chain Vb8.2, vb11 | B [auth D] | 241 | Mus musculus | Mutation(s): 0  | |
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
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Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 3 | |||||
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Molecule | Chains | Sequence Length | Organism | Details | Image |
Antigen-presenting glycoprotein CD1d1 | C [auth A] | 285 | Mus musculus | Mutation(s): 0  Gene Names: Cd1d1, mCG_3074 | |
UniProt & NIH Common Fund Data Resources | |||||
Find proteins for P11609 (Mus musculus) Explore P11609  Go to UniProtKB:  P11609 | |||||
IMPC:  MGI:107674 | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | P11609 | ||||
Sequence AnnotationsExpand | |||||
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Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 4 | |||||
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Molecule | Chains | Sequence Length | Organism | Details | Image |
Beta-2-microglobulin | D [auth B] | 99 | Mus musculus | Mutation(s): 0  Gene Names: B2m | |
UniProt & NIH Common Fund Data Resources | |||||
Find proteins for P01887 (Mus musculus) Explore P01887  Go to UniProtKB:  P01887 | |||||
IMPC:  MGI:88127 | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | P01887 | ||||
Sequence AnnotationsExpand | |||||
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Oligosaccharides
Small Molecules
Ligands 4 Unique | |||||
---|---|---|---|---|---|
ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
ELM Query on ELM | M [auth A] | N-[(2S,3S,4R)-3,4-dihydroxy-8-oxo-8-[(6-phenylhexyl)amino]-1-{[(2S,3R,4S,5R,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)tetra
hydro-2H-pyran-2-yl]oxy}octan-2-yl]dodecanamide C38 H66 N2 O10 IUMALAAYPYPBAP-RYYFEHCXSA-N | |||
PLM Query on PLM | J [auth A] | PALMITIC ACID C16 H32 O2 IPCSVZSSVZVIGE-UHFFFAOYSA-N | |||
NAG Query on NAG | K [auth A], L [auth A] | 2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N | |||
NA Query on NA | F [auth C], G [auth C], H [auth D], I [auth D], N [auth A] | SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.60 Å
- R-Value Free: 0.239 
- R-Value Work: 0.208 
- R-Value Observed: 0.209 
- Space Group: C 2 2 21
Unit Cell:
Length ( Å ) | Angle ( ˚ ) |
---|---|
a = 79.809 | α = 90 |
b = 191.115 | β = 90 |
c = 152.378 | γ = 90 |
Software Name | Purpose |
---|---|
REFMAC | refinement |
SCALEPACK | data scaling |
PDB_EXTRACT | data extraction |
HKL-2000 | data reduction |
PHASER | phasing |
Entry History 
Deposition Data
- Released Date: 2019-04-10  Deposition Author(s): Wang, J., Zajonc, D.
Revision History (Full details and data files)
- Version 1.0: 2019-04-10
Type: Initial release - Version 1.1: 2019-10-16
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: 2023-10-04
Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary