6O8D | pdb_00006o8d

Anti-CD28xCD3 CODV Fab bound to CD28

• PDB DOI: https://doi.org/10.2210/pdb6O8D/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Homo sapiens
• Expression System: Homo sapiens
• Mutation(s): No 


• Deposited: 2019-03-09 Released: 2019-11-20 
• Deposition Author(s): Lord, D.M., Wei, R.R.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.55 Å
• R-Value Free: 
  0.356 (Depositor), 0.354 (DCC) 
• R-Value Work: 
  0.272 (Depositor), 0.275 (DCC) 
• R-Value Observed: 
  0.281 (Depositor) 

Starting Models: experimental

Literature

Trispecific antibodies enhance the therapeutic efficacy of tumor-directed T cells through T cell receptor co-stimulation

Wu, L., Seung, E., Xu, L., Rao, E., Lord, D.M., Wei, R.R., Cortez-Retamozo, V., Ospina, B., Posternak, V., Ulinski, G., Piepenhagen, P., Francesconi, E., El Murr, N., Beil, C., Dabdoubi, T., Cameron, B., Bertrand, T., Ferrari, P., Pouzieux, S., Lemoine, C., Prades, C., Park, A., Qiu, H., Song, Z., Zhang, B., Sun, F., Chiron, M., Rao, S., Radosevic, K., Zhi-yong, Y., Nabel, G.J.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 91.25 kDa 
• Atom Count: 6,183 
• Modeled Residue Count: 796 
• Deposited Residue Count: 822 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
T-cell-specific surface glycoprotein CD28	A [auth C]	126	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
Glycosylation
Glycosylation Sites: 2		Go to GlyGen: P10747-1

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Anti-CD28xCD3 CODV Fab Light chain	B [auth L]	338	Homo sapiens	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Anti-CD28xCD3 CODV Fab Heavy chain	C [auth H]	358	Homo sapiens	Mutation(s): 0

Oligosaccharides

Help  

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	D [auth A]	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	E [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: 3.55 Å
• R-Value Free:  0.356 (Depositor), 0.354 (DCC) 
• R-Value Work:  0.272 (Depositor), 0.275 (DCC) 
• R-Value Observed: 0.281 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 153.14	α = 90
b = 60.139	β = 104.04
c = 152.558	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
Aimless	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2019-11-20 
Deposition Author(s): Lord, D.M., Wei, R.R.

Revision History  

• Version 1.0: 2019-11-20
  Type: Initial release
  
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Structure summary
• Version 2.1: 2023-10-11
  Changes: Data collection, Database references, Refinement description, Structure summary
• Version 2.2: 2024-11-20
  Changes: Structure summary