5AD0 | pdb_00005ad0

COMPLEX OF A B21 CHICKEN MHC CLASS I MOLECULE AND A 11MER CHICKEN PEPTIDE

• PDB DOI: https://doi.org/10.2210/pdb5AD0/pdb
• Entry: 5AD0 supersedes: 2YF1

• Classification: IMMUNE SYSTEM
• Organism(s): Gallus gallus
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2015-08-19 Released: 2016-09-28 
• Deposition Author(s): Chappell, P.E., Roversi, P., Harrison, M.C., Kaufman, J.F., Lea, S.M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.84 Å
• R-Value Free: 
  0.273 (Depositor), 0.290 (DCC) 
• R-Value Work: 
  0.236 (Depositor), 0.250 (DCC) 
• R-Value Observed: 
  0.238 (Depositor) 

Starting Model: experimental

Literature

Complex of a B21 Chicken Mhc Class I Molecule and a 11mer Chicken Peptide

Chappell, P.E., Roversi, P., Harrison, M.C., Kaufman, J.F., Lea, S.M.

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: 49.25 kDa 
• Atom Count: 3,063 
• Modeled Residue Count: 378 
• Deposited Residue Count: 438 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
MHC CLASS I ALPHA CHAIN 2	A	329	Gallus gallus	Mutation(s): 0
UniProt
Find proteins for Q95601 (Gallus gallus) Explore Q95601  Go to UniProtKB:  Q95601

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
BETA-2-MICROGLOBULIN	B	98	Gallus gallus	Mutation(s): 0
UniProt
Find proteins for P21611 (Gallus gallus) Explore P21611  Go to UniProtKB:  P21611

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
11MER PEPTIDE	C	11	Gallus gallus	Mutation(s): 0
UniProt
Find proteins for P01994 (Gallus gallus) Explore P01994  Go to UniProtKB:  P01994

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EDO	E [auth C], F [auth C]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
CA	D [auth C]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.84 Å
• R-Value Free:  0.273 (Depositor), 0.290 (DCC) 
• R-Value Work:  0.236 (Depositor), 0.250 (DCC) 
• R-Value Observed: 0.238 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 73.861	α = 90
b = 72.329	β = 90
c = 73.528	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
XDS	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-09-28 
Deposition Author(s): Chappell, P.E., Roversi, P., Harrison, M.C., Kaufman, J.F., Lea, S.M.
• This entry supersedes: 2YF1

Revision History  

• Version 1.0: 2016-09-28
  Type: Initial release
  
• Version 1.1: 2024-01-10
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description
• Version 1.2: 2024-10-23
  Changes: Structure summary