1KBG

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

Structural Biology Knowledgebase: 1KBG SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.279
  • R-Value Work: 0.224

Literature

Macromolecules
Sequence Display for 1KBG

Classification: IMMUNE SYSTEM

Total Structure Weight: 45460.28

Macromolecule Entities
Molecule Chains Length Organism Details
PROTEIN (MAJOR HISTOCOMPATIBILITY COMPLEX CLASS I ANTIGEN H-2KB) H 274 Mus musculus Fragment: PEPTIDE-BINDING DOMAIN
Details: FORMS HETERODIMER WITH CHAIN L, AND THEN A TRIMOLECULAR COMPLEX WITH CHAIN P
Gene Name(s): H2-K1 H2-K
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
PROTEIN (BETA-2-MICROGLOBULIN) L 99 Mus musculus Fragment: MHC ASSOCIATED LIGHT CHAIN
Details: FORMS HETERODIMER WITH CHAIN H, AND THEN A TRIMOLECULAR COMPLEX WITH CHAIN P
Gene Name(s): B2m
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
PROTEIN (SYNTHETIC GLYCOPEPTIDE RGY8-6H-GAL2) P 8 Vesicular stomatitis indiana virus Fragment: H-2KB-BOUND GLYCOPEPTIDE
Mutation: Q6X
Details: VSV-8 DERIVED GLYCOPEPTIDE THAT FORMS A TRIMOLECULAR COMPLEX WITH CHAINS H AND L.
Gene Name(s): N
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 4 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
NAG
Query on NAG

H N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
GLA
Query on GLA

P ALPHA D-GALACTOSE
C6 H12 O6
WQZGKKKJIJFFOK-PHYPRBDBSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
GAL
Query on GAL

P BETA-D-GALACTOSE
C6 H12 O6
WQZGKKKJIJFFOK-FPRJBGLDSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
FUC
Query on FUC

H ALPHA-L-FUCOSE
C6 H12 O5
SHZGCJCMOBCMKK-SXUWKVJYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
Modified Residues 1 Unique
ID Chains Type Formula 2D Diagram Parent
ESC
Query on ESC
P L-PEPTIDE LINKING C6 H13 N O2 S MET

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.279
  • R-Value Work: 0.224
  • Space Group: P 21 21 2

Unit Cell:

Length (Å) Angle (°)
a = 135.87 α = 90.00
b = 86.84 β = 90.00
c = 44.98 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 1998-08-28
  • Released Date: 1999-02-09
  • Deposition author(s): Speir, J.A., Abdel-Motal, U.M., Jondal, M., Wilson, I.A.

Revision History

  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4
  • 2011-07-13
    Type: Biological assembly | Details: Added software calculated values