1KTD

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

• PDB DOI: https://doi.org/10.2210/pdb1KTD/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Mus musculus, Columba livia
• Expression System: Spodoptera frugiperda
• Mutation(s): Yes 


• 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: 2.40 Å
• R-Value Free: 0.279 
• 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)

Biological Assembly 3  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 4-mer - A2B2 

Biological assembly 3 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 92.09 kDa 
• Atom Count: 6,814 
• Modelled Residue Count: 794 
• Deposited Residue Count: 794 
• 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  Gene Names: H2-Ea
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	215	Columba livia, Mus musculus This entity is chimeric	Mutation(s): 1  Gene Names: CYC, H2-Eb1
UniProt & NIH Common Fund Data Resources
Find proteins for P00021 (Columba livia) Explore P00021  Go to UniProtKB:  P00021
Find proteins for P04230 (Mus musculus) Explore P04230  Go to UniProtKB:  P04230
IMPC:  MGI:95901
UniProt Groups	P00021P04230

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	E [auth A], F [auth A], G [auth B], I [auth C]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
SO4	H [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.279 
• R-Value Work: 0.220 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 145.52	α = 90
b = 57.3	β = 94.23
c = 116.57	γ = 90

Software Package:

Software Name	Purpose
bioteX	data collection
bioteX	data reduction
AMoRE	phasing
CNS	refinement
bioteX	data scaling

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 1.3: 2017-06-21
  Changes: Advisory, Database references, Source and taxonomy
• Version 1.4: 2017-10-11
  Changes: Refinement description
• Version 1.5: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Derived calculations, Structure summary