2Q7Y

Structure of the endogenous iNKT cell ligand iGb3 bound to mCD1d

PDB DOI: https://doi.org/10.2210/pdb2Q7Y/pdb

Classification: IMMUNE SYSTEM
Organism(s): Mus musculus
Expression System: Drosophila melanogaster
Mutation(s): Yes

Deposited: 2007-06-07 Released: 2008-04-01
Deposition Author(s): Zajonc, D.M., Wilson, I.A., Teyton, L.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.95 Å
R-Value Free: 0.245
R-Value Work: 0.199
R-Value Observed: 0.200

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: 93.35 kDa
Atom Count: 6,589
Modelled Residue Count: 734
Deposited Residue Count: 768
Unique protein chains: 2

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
T-cell surface glycoprotein CD1d1	A, C	285	Mus musculus	Mutation(s): 0 Gene Names: Cd1d1, Cd1.1
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

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-2-microglobulin	B, D	99	Mus musculus	Mutation(s): 1 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 Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	E, G	2		N-Glycosylation	Interactions Focus chain E Focus chain G Interactions & Density Focus chain E Focus chain G
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	F	5		N-Glycosylation	Interactions Focus chain F Interactions & Density Focus chain F
Glycosylation Resources
GlyTouCan: G22768VO GlyCosmos: G22768VO GlyGen: G22768VO

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
IGC Query on IGC Download Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain M [auth C] MOL2 format, chain I [auth A] MOL2 format, chain M [auth C]	I [auth A], M [auth C]	N-[(1S,2R,3E)-1-({[ALPHA-D-GALACTOPYRANOSYL-(1->3)-BETA-D-GALACTOPYRANOSYL-(1->4)-BETA-D-GLUCOPYRANOSYL]OXY}METHYL)-2-H YDROXYHEPTADEC-3-EN-1-YL]OCTANAMIDE C₄₄ H₈₁ N O₁₈ RWHPBLFPAUXKDB-WOYQYECOSA-N		Interactions Focus chain I [auth A] Focus chain M [auth C] Interactions & Density Focus chain I [auth A] Focus chain M [auth C]
PLM Query on PLM Download Ideal Coordinates CCD File SDF format, chain J [auth A] SDF format, chain N [auth C] MOL2 format, chain J [auth A] MOL2 format, chain N [auth C]	J [auth A], N [auth C]	PALMITIC ACID C₁₆ H₃₂ O₂ IPCSVZSSVZVIGE-UHFFFAOYSA-N		Interactions Focus chain J [auth A] Focus chain N [auth C] Interactions & Density Focus chain J [auth A] Focus chain N [auth C]
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain K [auth C] SDF format, chain L [auth C] MOL2 format, chain H [auth A] MOL2 format, chain K [auth C] MOL2 format, chain L [auth C]	H [auth A], K [auth C], L [auth C]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain H [auth A] Focus chain K [auth C] Focus chain L [auth C] Interactions & Density Focus chain H [auth A] Focus chain K [auth C] Focus chain L [auth C]

Binding Affinity Annotations
ID	Source	Binding Affinity
IGC	PDBBind: 2Q7Y	Kd: 5.00e+4 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.95 Å
R-Value Free: 0.245
R-Value Work: 0.199
R-Value Observed: 0.200
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.941	α = 90
b = 96.224	β = 106.23
c = 77.926	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
HKL-2000	data reduction
HKL-2000	data scaling
AMoRE	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2008-04-01

Deposition Author(s):

Zajonc, D.M.

Wilson, I.A.

Teyton, L.

Revision History (Full details and data files)

Version 1.0: 2008-04-01
Type: Initial release
Version 1.1: 2011-07-13
Changes: Non-polymer description, Version format compliance
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Structure summary
Version 2.1: 2023-08-30
Changes: Data collection, Database references, Refinement description, Structure summary