4Y4F

Crystal structure of the mCD1d/GCK127/iNKTCR ternary complex

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.19 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.218 
  • R-Value Observed: 0.219 

wwPDB Validation   3D Report Full Report


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 CD1d1
A, E
285Mus musculusMutation(s): 1 
Gene Names: Cd1d1, Cd1.1
UniProt & NIH Common Fund Data Resources
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IMPC:  MGI:107674
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UniProt GroupP11609
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Beta-2-microglobulin
B, F
99Mus musculusMutation(s): 0 
Gene Names: B2m
UniProt & NIH Common Fund Data Resources
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IMPC:  MGI:88127
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UniProt GroupP01887
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Chimeric TCR Valpha14/Jalpha18 chain (mouse variable domain/ human constant domain)
C, G
209Mus musculus, Homo sapiens
This entity is chimeric		Mutation(s): 0 
Gene Names: Trav11, Trav11d
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PHAROS:  P01848
Find proteins for A0A0B4J1J9 (Mus musculus)
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UniProt GroupsP01848A0A0B4J1J9
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Chimeric TCR Vbeta8.2 chain (mouse variable domain, human constant domain)
D, H
241Mus musculus, Homo sapiens
This entity is chimeric		Mutation(s): 0 
Gene Names: TRBC2, TCRBC2
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PHAROS:  A0A5B9
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UniProt GroupsA0A5B9A2NTY6
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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
I, J
2N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
49M
Query on 49M
Download Ideal Coordinates CCD File 
L [auth A],
N [auth E]		(1R)-1,5-anhydro-1-[(1E,3S,4S,5R)-4,5-dihydroxy-3-(nonacosanoylamino)nonadec-1-en-1-yl]-D-galactitol
C54 H105 N O8
CSICITALHNIXPU-MSSILZRDSA-N
NAG
Query on NAG
Download Ideal Coordinates CCD File 
K [auth A],
M [auth E]		2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.19 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.218 
  • R-Value Observed: 0.219 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 78.589α = 90
b = 149.728β = 96.46
c = 101.386γ = 90
Software Package:
Software NamePurpose
Blu-Icedata collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
Cootmodel building
REFMACrefinement
PDB_EXTRACTdata extraction

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesAI074952

Revision History  (Full details and data files)

  • Version 1.0: 2015-05-27
    Type: Initial release
  • Version 1.1: 2017-09-13
    Changes: Author supporting evidence, Derived calculations, Source and taxonomy, Structure summary
  • Version 1.2: 2019-12-11
    Changes: Author supporting evidence
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Structure summary
  • Version 2.1: 2023-09-27
    Changes: Data collection, Database references, Refinement description, Structure summary