3TN0

Structure of mouse Va14Vb8.2NKT TCR-mouse CD1d-a-C-Galactosylceramide complex

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 0.289 
  • R-Value Work: 0.225 
  • R-Value Observed: 0.229 

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Ligand Structure Quality Assessment 


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



Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Antigen-presenting glycoprotein CD1d1302Mus musculusMutation(s): 0 
Gene Names: Cd1d1, Cd1.1
UniProt & NIH Common Fund Data Resources
Find proteins for P11609 (Mus musculus)
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Go to UniProtKB:  P11609
IMPC:  MGI:107674
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UniProt GroupP11609
Sequence Annotations
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Beta-2 microglobulin99Mus musculusMutation(s): 0 
Gene Names: B2m, RP23-34E24.5-001, mCG_11606
UniProt & NIH Common Fund Data Resources
Find proteins for P01887 (Mus musculus)
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IMPC:  MGI:88127
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UniProt GroupP01887
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
mouse NKT Valpha14 (MOUSE VARIABLE DOMAIN, HUMAN CONSTANT DOMAIN)207Homo sapiens, Mus musculus
This entity is chimeric		Mutation(s): 0 
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PHAROS:  P01848
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UniProt GroupP01848
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
mouse NKT Vbeta8.2 (MOUSE VARIABLE DOMAIN, HUMAN CONSTANT DOMAIN)244Homo sapiens, Mus musculus
This entity is chimeric		Mutation(s): 0 
UniProt
Find proteins for P01850 (Homo sapiens)
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UniProt GroupP01850
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Oligosaccharides

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Entity ID: 5
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
E
2N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
QUX
Query on QUX
Download Ideal Coordinates CCD File 
F [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
NAG
Query on NAG
Download Ideal Coordinates CCD File 
G [auth A],
H [auth A]		2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
QUX PDBBind:  3TN0 Kd: 2200 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 0.289 
  • R-Value Work: 0.225 
  • R-Value Observed: 0.229 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 59.171α = 90
b = 86.368β = 90
c = 236.403γ = 90
Software Package:
Software NamePurpose
Blu-Icedata collection
PHASERphasing
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-12-14
    Type: Initial release
  • 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: 2023-09-13
    Changes: Advisory, Data collection, Database references, Refinement description, Structure summary