6MIY
Crystal structure of the mCD1d/xxa (JJ239)/iNKTCR ternary complex
- PDB DOI: https://doi.org/10.2210/pdb6MIY/pdb
- Classification: IMMUNE SYSTEM
- Organism(s): Mus musculus, Homo sapiens
- Expression System: Escherichia coli BL21(DE3), Spodoptera frugiperda
- Mutation(s): Yes 
- Deposited: 2018-09-20 Released: 2019-01-09 
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.75 Å
- R-Value Free: 0.247 
- R-Value Work: 0.192 
- R-Value Observed: 0.194 
wwPDB Validation   3D Report Full Report
Currently 6MIY does not have a validation slider image.
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 |
T cell receptor alpha variable 11,T cell receptor alpha variable 11,T cell receptor alpha joining 18,Human nkt tcr alpha chain, CHIMERIC PROTEIN | A [auth C], F [auth G] | 209 | Mus musculus, Homo sapiens | Mutation(s): 0  Gene Names: Trav11, Trav11d, Traj18, B2M, HDCMA22P | |
UniProt | |||||
Find proteins for A0A0B4J1J9 (Mus musculus) Explore A0A0B4J1J9  Go to UniProtKB:  A0A0B4J1J9 | |||||
Find proteins for K7N5M3 (Homo sapiens) Explore K7N5M3  Go to UniProtKB:  K7N5M3 | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Groups | K7N5M3A0A0B4J1J9 | ||||
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 |
Beta-chain,T cell receptor chain,T cell receptor beta constant 2, CHIMERIC PROTEIN | B [auth D], G [auth H] | 241 | Mus musculus, Homo sapiens | Mutation(s): 2  | |
UniProt & NIH Common Fund Data Resources | |||||
Find proteins for A0N8J3 (Mus musculus) Explore A0N8J3  Go to UniProtKB:  A0N8J3 | |||||
Find proteins for A2NTY6 (Mus musculus) Explore A2NTY6  Go to UniProtKB:  A2NTY6 | |||||
Find proteins for A0A5B9 (Homo sapiens) Explore A0A5B9  Go to UniProtKB:  A0A5B9 | |||||
PHAROS:  A0A5B9 | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Groups | A0N8J3A0A5B9A2NTY6 | ||||
Sequence AnnotationsExpand | |||||
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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], E | 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], H [auth F] | 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 | |
JTV Query on JTV | R [auth A], U [auth E] | N-{(2S,3S,4R)-1-[(4-O-benzyl-alpha-D-galactopyranosyl)oxy]-3,4-dihydroxyoctadecan-2-yl}hexacosanamide C57 H105 N O9 XDALVMZANJGPPV-VSVWWTSQSA-N | |||
GOL Query on GOL | S [auth A], T [auth A], V [auth E], W [auth G] | GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N | |||
CL Query on CL | Q [auth D] | CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M | |||
NA Query on NA | O [auth C], P [auth D], X [auth G], Y [auth H] | SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.75 Å
- R-Value Free: 0.247 
- R-Value Work: 0.192 
- R-Value Observed: 0.194 
- Space Group: C 1 2 1
Unit Cell:
Length ( Å ) | Angle ( ˚ ) |
---|---|
a = 78.865 | α = 90 |
b = 192.477 | β = 90.79 |
c = 150.418 | γ = 90 |
Software Name | Purpose |
---|---|
HKL-2000 | data scaling |
REFMAC | refinement |
PDB_EXTRACT | data extraction |
HKL-2000 | data reduction |
PHASER | phasing |
Structure Validation
View Full Validation Report
Currently 6MIY does not have a validation slider image.
Entry History 
Deposition Data
- Released Date: 2019-01-09  Deposition Author(s): Zajonc, D.M., Bitra, A., Janssens, J.
Revision History (Full details and data files)
- Version 1.0: 2019-01-09
Type: Initial release - Version 1.1: 2019-01-16
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: 2023-10-11
Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary