8SJK

Pembrolizumab Caffeine crystal

• PDB DOI: https://doi.org/10.2210/pdb8SJK/pdb

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


• Deposited: 2023-04-18 Released: 2024-04-24 
• Deposition Author(s): Larpent, P., Codan, L., Bothe, J.R., Stueber, D., Reichert, P., Fischmann, T., Su, Y., Pabit, S., Gupta, S., Iuzzolino, L., Cote, A.
• Funding Organization(s): Other private

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.22 Å
• R-Value Free: 0.238 
• R-Value Work: 0.186 
• R-Value Observed: 0.189 

Literature

Smaall angle X-ray scattering as powerful toolsfor phase and crystallinity assessment of monoclonal antibodies crystallites in support of batch crystallization and processing

Larpent, P., Codan, L., Bothe, J.R., Stueber, D., Reichert, P., Fischmann, T.O., Su, Y., Pabit, S., Gupta, S., Iuzzolino, L., Cote, A.

To be published.

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 Evidence: electron microscopy

Macromolecule Content

• Total Structure Weight: 75.13 kDa 
• Atom Count: 5,415 
• Modelled Residue Count: 641 
• Deposited Residue Count: 662 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ANTIBODY LIGHT CHAIN	A	218	Homo sapiens	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
ANTIBODY HEAVY CHAIN	B	444	Homo sapiens	Mutation(s): 0

Oligosaccharides

Help

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	C [auth D]	7		N-Glycosylation

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-fructofuranose-(2-1)-alpha-D-glucopyranose	D [auth E], E [auth F]	2		N/A

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CFF (Subject of Investigation/LOI)	F [auth A]	CAFFEINE C8 H10 N4 O2 RYYVLZVUVIJVGH-UHFFFAOYSA-N

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 4
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900003	D [auth E], E [auth F]	sucrose	Oligosaccharide / Nutrient

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.22 Å
• R-Value Free: 0.238 
• R-Value Work: 0.186 
• R-Value Observed: 0.189 
• Space Group: P 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 43.8	α = 90
b = 113.9	β = 90
c = 175	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
XDS	data reduction
MOLREP	phasing
Aimless	data scaling

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-04-24 
Deposition Author(s): Larpent, P., Codan, L., Bothe, J.R., Stueber, D., Reichert, P., Fischmann, T., Su, Y., Pabit, S., Gupta, S., Iuzzolino, L., Cote, A.

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Funding Organization	Location	Grant Number
Other private	United States	--

Revision History  

• Version 1.0: 2024-04-24
  Type: Initial release