3VWK
Ternary crystal structure of the human NKT TCR-CD1d-4'deoxy-alpha-galactosylceramide complex
- PDB DOI: https://doi.org/10.2210/pdb3VWK/pdb
- Classification: IMMUNE SYSTEM
- Organism(s): Homo sapiens
- Expression System: Trichoplusia ni, Escherichia coli
- Mutation(s): No 
- Deposited: 2012-08-24 Released: 2012-10-03 
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.94 Å
- R-Value Free: 0.250 
- R-Value Work: 0.191 
- R-Value Observed: 0.194 
This is version 1.4 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 |
Antigen-presenting glycoprotein CD1d | 284 | Homo sapiens | Mutation(s): 0  Gene Names: CD1D | ||
UniProt & NIH Common Fund Data Resources | |||||
Find proteins for P15813 (Homo sapiens) Explore P15813  Go to UniProtKB:  P15813 | |||||
PHAROS:  P15813 GTEx:  ENSG00000158473  | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | P15813 | ||||
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 |
Beta-2-microglobulin | 99 | Homo sapiens | Mutation(s): 0  Gene Names: B2M, CDABP0092, HDCMA22P | ||
UniProt & NIH Common Fund Data Resources | |||||
Find proteins for P61769 (Homo sapiens) Explore P61769  Go to UniProtKB:  P61769 | |||||
PHAROS:  P61769 GTEx:  ENSG00000166710  | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | P61769 | ||||
Sequence AnnotationsExpand | |||||
|
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 3 | |||||
---|---|---|---|---|---|
Molecule | Chains | Sequence Length | Organism | Details | Image |
NKT15 T cell receptor alpha-chain | 209 | Homo sapiens | Mutation(s): 0  | ||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
Sequence AnnotationsExpand | |||||
|
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 4 | |||||
---|---|---|---|---|---|
Molecule | Chains | Sequence Length | Organism | Details | Image |
NKT15 T cell receptor beta-chain | 246 | Homo sapiens | Mutation(s): 0  | ||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
Sequence AnnotationsExpand | |||||
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Small Molecules
Ligands 3 Unique | |||||
---|---|---|---|---|---|
ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
4GH Query on 4GH | G [auth A] | N-{(2S,3R)-1-[(4-deoxy-alpha-D-xylo-hexopyranosyl)oxy]-3-hydroxyoctadecan-2-yl}hexacosanamide C50 H99 N O7 SBJWEMJDCMAIOT-AHRAGLCISA-N | |||
NAG Query on NAG | E [auth A], F [auth A] | 2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N | |||
MG Query on MG | H [auth D] | MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.94 Å
- R-Value Free: 0.250 
- R-Value Work: 0.191 
- R-Value Observed: 0.194 
- Space Group: C 2 2 2
Unit Cell:
Length ( Å ) | Angle ( ˚ ) |
---|---|
a = 144.27 | α = 90 |
b = 177.26 | β = 90 |
c = 83.75 | γ = 90 |
Software Name | Purpose |
---|---|
Blu-Ice | data collection |
PHASER | phasing |
PHENIX | refinement |
MOSFLM | data reduction |
SCALA | data scaling |
Entry History 
Deposition Data
- Released Date: 2012-10-03  Deposition Author(s): Wun, K.S., Rossjohn, J.
Revision History (Full details and data files)
- Version 1.0: 2012-10-03
Type: Initial release - Version 1.1: 2012-10-17
Changes: Structure summary - Version 1.2: 2013-08-14
Changes: Database references - Version 1.3: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Data collection, Database references, Derived calculations, Structure summary - Version 1.4: 2023-11-08
Changes: Data collection, Database references, Refinement description, Structure summary