1KBG

MHC Class I H-2KB Presented Glycopeptide RGY8-6H-GAL2

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.279 
  • R-Value Work: 0.224 
  • R-Value Observed: 0.224 

wwPDB Validation   3D Report Full Report


This is version 2.3 of the entry. See complete history. 



Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
PROTEIN (MAJOR HISTOCOMPATIBILITY COMPLEX CLASS I ANTIGEN H-2KB)A [auth H]274Mus musculusMutation(s): 0 
UniProt
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Go to UniProtKB:  P01901
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UniProt GroupP01901
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
PROTEIN (BETA-2-MICROGLOBULIN)B [auth L]99Mus musculusMutation(s): 0 
UniProt & NIH Common Fund Data Resources
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IMPC:  MGI:88127
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UniProt GroupP01887
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  • Reference Sequence

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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
PROTEIN (SYNTHETIC GLYCOPEPTIDE RGY8-6H-GAL2)C [auth P]8N/AMutation(s): 1 
UniProt
Find proteins for P11212 (Vesicular stomatitis Indiana virus (strain Glasgow))
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Entity Groups  
UniProt GroupP11212
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Oligosaccharides

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Entity ID: 4
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranoseD [auth A]3N-Glycosylation
Glycosylation Resources
GlyTouCan:  G21290RB
GlyCosmos:  G21290RB
GlyGen:  G21290RB
Entity ID: 5
MoleculeChains Length2D Diagram Glycosylation3D Interactions
alpha-D-galactopyranose-(1-4)-beta-D-galactopyranoseE [auth B]2N/A
Glycosylation Resources
GlyTouCan:  G67988RO
GlyCosmos:  G67988RO
GlyGen:  G67988RO
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG
Download Ideal Coordinates CCD File 
F [auth H]2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
ESC
Query on ESC		C [auth P]L-PEPTIDE LINKINGC6 H13 N O2 SMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.279 
  • R-Value Work: 0.224 
  • R-Value Observed: 0.224 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 135.87α = 90
b = 86.84β = 90
c = 44.98γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
X-PLORmodel building
X-PLORrefinement
X-PLORphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1999-02-09
    Type: Initial release
  • Version 1.1: 2007-10-21
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Structure summary
  • Version 2.1: 2021-11-03
    Changes: Database references, Structure summary
  • Version 2.2: 2023-08-16
    Changes: Data collection, Refinement description
  • Version 2.3: 2023-11-15
    Changes: Data collection