3SDD

Crystal structure of autoreactive-Valpha14-Vbeta6 NKT TCR in complex with CD1d-beta-lactosylceramide

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.318 
  • R-Value Work: 0.258 
  • R-Value Observed: 0.261 

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Ligand Structure Quality Assessment 


This is version 2.0 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: Cd1.1, Cd1d1
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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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Beta-2-microglobulin99Mus musculusMutation(s): 0 
Gene Names: B2m
UniProt & NIH Common Fund Data Resources
Find proteins for P01887 (Mus musculus)
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Go to UniProtKB:  P01887
IMPC:  MGI:88127
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UniProt GroupP01887
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
NKT TCR Valpha14 chain207Mus musculus, Homo sapiens
This entity is chimeric		Mutation(s): 0 
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Find proteins for P01848 (Homo sapiens)
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Go to UniProtKB:  P01848
PHAROS:  P01848
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UniProt GroupP01848
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
NKT TCR autoreactive-Vbeta6 chain245Mus musculus, Homo sapiens
This entity is chimeric		Mutation(s): 0 
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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
3GD
Query on 3GD
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H [auth A]N-[(2S,3R,4E)-1-{[4-O-(beta-D-galactopyranosyl)-beta-D-glucopyranosyl]oxy}-3-hydroxyoctadec-4-en-2-yl]docosanamide
C52 H99 N O13
QYWVASPEUXEHSY-NNRNTGNWSA-N
NAG
Query on NAG
Download Ideal Coordinates CCD File 
F [auth A],
G [auth A]		2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
3GD PDBBind:  3SDD Kd: 4840 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.318 
  • R-Value Work: 0.258 
  • R-Value Observed: 0.261 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 94.469α = 90
b = 94.469β = 90
c = 291.063γ = 90
Software Package:
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction

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: 2011-10-05
    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