1KPU

High resolution crystal structure of the MHC class I complex H-2Kb/VSV8

Structural Biology Knowledgebase: 1KPU SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.5 Å
  • R-Value Free: 0.208
  • R-Value Work: 0.184

Literature

Macromolecules
Sequence Display for 1KPU

Classification: IMMUNE SYSTEM

Total Structure Weight: 45337.24

Macromolecule Entities
Molecule Chains Length Organism Details
H-2 class I histocompatibility antigen, K-B alpha chain A 274 Mus musculus Fragment: extracellular domain, sequence database residues 22-295, numbered 1-274
Gene Name(s): H2-K1 H2-K
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
beta-2-microglobulin B 99 Mus musculus Fragment: sequence database residues 21-119, numbered 1-99
Gene Name(s): B2m
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
nucleocapsid P 8 Vesicular stomatitis indiana virus Fragment: sequence database residues 52-59, numbered 1-8
Gene Name(s): N
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

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

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

A ALPHA-L-FUCOSE
C6 H12 O5
SHZGCJCMOBCMKK-SXUWKVJYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MPD
Query on MPD

A, B (4S)-2-METHYL-2,4-PENTANEDIOL
C6 H14 O2
SVTBMSDMJJWYQN-YFKPBYRVSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.5 Å
  • R-Value Free: 0.208
  • R-Value Work: 0.184
  • Space Group: P 21 21 2
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 136.09 α = 90.00
b = 88.12 β = 90.00
c = 45.24 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2002-01-02
  • Released Date: 2003-06-10
  • Deposition author(s): Rudolph, M.G., Wilson, I.A.

Revision History

  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4
  • 2011-07-13
    Type: Non-polymer description | Details: chemical name/synonym update