3QUX

Structure of the mouse CD1d-alpha-C-GalCer-iNKT TCR complex

PDB DOI: https://doi.org/10.2210/pdb3QUX/pdb

Classification: IMMUNE SYSTEM
Organism(s): Mus musculus
Expression System: Spodoptera frugiperda, Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2011-02-24 Released: 2011-06-29
Deposition Author(s): Li, Y., Girardi, E., Yu, E.D., Zajonc, D.M.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.91 Å
R-Value Free: 0.252
R-Value Work: 0.208
R-Value Observed: 0.210

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.1 of the entry. See complete history.

Macromolecule Content

Total Structure Weight: 96.24 kDa
Atom Count: 6,470
Modelled Residue Count: 804
Deposited Residue Count: 834
Unique protein chains: 4

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Antigen-presenting glycoprotein CD1d1	A	285	Mus musculus	Mutation(s): 0 Gene Names: Cd1.1, CD1d, Cd1d1
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 Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-2 microglobulin	B	99	Mus musculus	Mutation(s): 0 Gene Names: B2m, beta-2-microglobulin, mCG_11606, RP23-34E24.5-001
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 Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Valpha14 (mouse variable domain, human constant domain)	C	209	Mus musculus	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P01848 (Homo sapiens) Explore P01848 Go to UniProtKB: P01848
PHAROS: P01848
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P01848
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Vbeta8.2 (mouse variable domain, human constant domain)	D	241	Mus musculus	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
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 Group	A0A5B9
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

Help

Entity ID: 5
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose	E	3		N-Glycosylation	Interactions Focus chain E Interactions & Density Focus chain E
Glycosylation Resources
GlyTouCan: G21290RB GlyCosmos: G21290RB GlyGen: G21290RB

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
QUX Query on QUX Download Ideal Coordinates CCD File SDF format, chain H [auth A] MOL2 format, chain H [auth A]	H [auth A]	N-[(3S,4S,5R)-4,5-dihydroxy-1-[(2R,3R,4R,5R,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]nonadecan-3-yl]hexacosanamide C₅₁ H₁₀₁ N O₈ BNYLLEHBKIGJHB-XHSUSRKPSA-N		Interactions Focus chain H [auth A] Interactions & Density Focus chain H [auth A]
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain G [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A]	F [auth A], G [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain F [auth A] Focus chain G [auth A] Interactions & Density Focus chain F [auth A] Focus chain G [auth A]

Binding Affinity Annotations
ID	Source	Binding Affinity
QUX	PDBBind: 3QUX	Kd: 247 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.91 Å
R-Value Free: 0.252
R-Value Work: 0.208
R-Value Observed: 0.210
Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 78.502	α = 90
b = 189.919	β = 90
c = 150.801	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
MOLREP	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2011-06-29

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2011-06-29
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Data collection, Database references, Derived calculations, Structure summary
Version 2.1: 2023-09-13
Changes: Data collection, Database references, Refinement description, Structure summary