1KT2

CRYSTAL STRUCTURE OF CLASS II MHC MOLECULE IEK BOUND TO MOTH CYTOCHROME C PEPTIDE

• PDB DOI: https://doi.org/10.2210/pdb1KT2/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Mus musculus, Lonomia obliqua
• Expression System: Spodoptera frugiperda
• Mutation(s): No 


• Deposited: 2002-01-15 Released: 2002-05-01 
• Deposition Author(s): Fremont, D.H., Dai, S., Chiang, H., Crawford, F., Marrack, P., Kappler, J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 0.294 
• R-Value Work: 0.220 

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

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

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 92.52 kDa 
• Atom Count: 6,743 
• Modelled Residue Count: 790 
• Deposited Residue Count: 790 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
H-2 class II histocompatibility antigen, E-D alpha chain	A, C	182	Mus musculus	Mutation(s): 0
UniProt
Find proteins for P01904 (Mus musculus) Explore P01904  Go to UniProtKB:  P01904

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Fusion protein consisting of cytochrome C peptide, glycine rich linker, and MHC E-beta-k	B, D	213	Lonomia obliqua, Mus musculus This entity is chimeric	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P04230 (Mus musculus) Explore P04230  Go to UniProtKB:  P04230
IMPC:  MGI:95901

Oligosaccharides

Help

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	E	2		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT GlyCosmos:  G42666HT GlyGen:  G42666HT

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	F [auth A], G [auth A], H [auth C], I [auth D]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 0.294 
• R-Value Work: 0.220 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 147.79	α = 90
b = 56.93	β = 92.12
c = 115.99	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing
CNS	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2002-05-01 
Deposition Author(s): Fremont, D.H., Dai, S., Chiang, H., Crawford, F., Marrack, P., Kappler, J.

Revision History  

• Version 1.0: 2002-05-01
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Non-polymer description, Version format compliance
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary