1YJD

Crystal structure of human CD28 in complex with the Fab fragment of a mitogenic antibody (5.11A1)

• PDB DOI: https://doi.org/10.2210/pdb1YJD/pdb

• Classification: IMMUNE SYSTEM/SIGNALING PROTEIN
• Organism(s): Mus musculus, Homo sapiens
• Expression System: Cricetulus griseus
• Mutation(s): No 


• Deposited: 2005-01-14 Released: 2005-02-15 
• Deposition Author(s): Evans, E.J., Esnouf, R.M., Manso-Sancho, R., Gilbert, R.J.C., James, J.R., Sorensen, P., Stuart, D.I., Davis, S.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 0.282 
• R-Value Work: 0.239 
• R-Value Observed: 0.248 

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 6-mer - A2B2C2 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 63.95 kDa 
• Atom Count: 4,493 
• Modelled Residue Count: 547 
• Deposited Residue Count: 574 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Fab fragment of 5.11A1 antibody light chain	A [auth L]	212	Mus musculus	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Fab fragment of 5.11A1 antibody heavy chain	B [auth H]	222	Mus musculus	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
T-cell-specific surface glycoprotein CD28	C	140	Homo sapiens	Mutation(s): 0  Gene Names: CD28
UniProt & NIH Common Fund Data Resources
Find proteins for P10747 (Homo sapiens) Explore P10747  Go to UniProtKB:  P10747
PHAROS:  P10747 GTEx:  ENSG00000178562

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 0.282 
• R-Value Work: 0.239 
• R-Value Observed: 0.248 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 191.219	α = 90
b = 47.417	β = 94.45
c = 71.842	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
PDB_EXTRACT	data extraction
DENZO	data reduction
SCALEPACK	data scaling
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-02-15 
Deposition Author(s): Evans, E.J., Esnouf, R.M., Manso-Sancho, R., Gilbert, R.J.C., James, J.R., Sorensen, P., Stuart, D.I., Davis, S.J.

Revision History  

• Version 1.0: 2005-02-15
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Non-polymer description, Version format compliance
• Version 1.3: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Database references, Derived calculations, Structure summary