1VGK

The crystal structure of class I Major histocompatibility complex, H-2Kd at 2.0 A resolution

• PDB DOI: https://doi.org/10.2210/pdb1VGK/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Mus musculus, Homo sapiens
• Expression System: Escherichia coli, Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2004-04-27 Released: 2005-06-28 
• Deposition Author(s): Zhou, M., Xu, Y., Liu, Y., Gao, G.F., Tien, P., Rao, Z.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.06 Å
• R-Value Free: 0.240 
• R-Value Work: 0.190 
• R-Value Observed: 0.192 

Literature

The crystal structure of class I major histocompatibility complex, H-2Kd at 2.0 A resolution

Zhou, M., Xu, Y., Liu, Y., Gao, G.F., Tien, P., Rao, Z.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 44.73 kDa 
• Atom Count: 3,583 
• Modelled Residue Count: 382 
• Deposited Residue Count: 382 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
H-2 class I histocompatibility antigen, K-D alpha chain	A	274	Mus musculus	Mutation(s): 0
UniProt
Find proteins for P01902 (Mus musculus) Explore P01902  Go to UniProtKB:  P01902

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-2-microglobulin	B	99	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P61769 (Homo sapiens) Explore P61769  Go to UniProtKB:  P61769
PHAROS:  P61769 GTEx:  ENSG00000166710

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
syvntnmgl	C	9	N/A	Mutation(s): 0

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.06 Å
• R-Value Free: 0.240 
• R-Value Work: 0.190 
• R-Value Observed: 0.192 
• Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 89.082	α = 90
b = 110.389	β = 90
c = 47.015	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
SCALEPACK	data scaling
CNS	refinement
HKL-2000	data reduction
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-06-28 
Deposition Author(s): Zhou, M., Xu, Y., Liu, Y., Gao, G.F., Tien, P., Rao, Z.

Revision History  

• Version 1.0: 2005-06-28
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2023-12-27
  Changes: Data collection, Database references
• Version 1.4: 2024-11-13
  Changes: Structure summary