5DK3 | pdb_00005dk3

Crystal Structure of Pembrolizumab, a full length IgG4 antibody

• PDB DOI: https://doi.org/10.2210/pdb5DK3/pdb

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


• Deposited: 2015-09-02 Released: 2015-11-18 
• Deposition Author(s): Scapin, G., Prosise, W., Reichert, P.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.28 Å
• R-Value Free: 
  0.224 (Depositor), 0.232 (DCC) 
• R-Value Work: 
  0.184 (Depositor), 0.199 (DCC) 
• R-Value Observed: 
  0.186 (Depositor) 

Literature

Structure of full-length human anti-PD1 therapeutic IgG4 antibody pembrolizumab.

Scapin, G., Yang, X., Prosise, W.W., McCoy, M., Reichert, P., Johnston, J.M., Kashi, R.S., Strickland, C.

(2015) Nat Struct Mol Biol 22: 953-958

• PubMed: 26595420 
• DOI: https://doi.org/10.1038/nsmb.3129
• Primary Citation Related Structures: 
  5DK3


• PubMed Abstract: 
  

  Immunoglobulin G4 antibodies exhibit unusual properties with important biological consequences. We report the structure of the human full-length IgG4 S228P anti-PD1 antibody pembrolizumab, solved to 2.3-Å resolution. Pembrolizumab is a compact molecule, consistent with the presence of a short hinge region. The Fc domain is glycosylated at the CH2 domain on both chains, but one CH2 domain is rotated 120° with respect to the conformation observed in all reported structures to date, and its glycan chain faces the solvent. We speculate that this new conformation is driven by the shorter hinge. The structure suggests a role for the S228P mutation in preventing the IgG4 arm exchange. In addition, this unusual Fc conformation suggests possible structural diversity between IgG subclasses and shows that use of isolated antibody fragments could mask potentially important interactions, owing to molecular flexibility.

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Organizational Affiliation: 
• Structural Chemistry, Merck &Co., Inc., Kenilworth, New Jersey, USA.
Biologics and Vaccines Formulation, Analytical Method Development, Merck &Co, Inc., Kenilworth, New Jersey, USA.
Bioprocess Technology and Expression, Merck &Co., Inc., Kenilworth, New Jersey, USA.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 4-mer - A2B2 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 4-mer - A2B1C1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 149.95 kDa 
• Atom Count: 10,749 
• Modeled Residue Count: 1,315 
• Deposited Residue Count: 1,324 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Light Chain	A, C [auth F]	218	Homo sapiens	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Heavy Chain	B, D [auth G]	444	Homo sapiens	Mutation(s): 0

Oligosaccharides

Help  

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	D 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	E [auth C]	7		N/A
Glycosylation Resources
GlyTouCan: G39213VZ GlyCosmos: G39213VZ GlyGen: G39213VZ

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose	F [auth D]	7		N-Glycosylation
Glycosylation Resources
GlyTouCan: G45889JQ GlyCosmos: G45889JQ GlyGen: G45889JQ

Entity ID: 5
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
beta-D-fructofuranose-(2-1)-alpha-D-glucopyranose	G [auth E], H, I	2		N/A
Glycosylation Resources
GlyTouCan: G05551OP GlyCosmos: G05551OP

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	J [auth A], K [auth B], L [auth B], M [auth B], N [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Biologically Interesting Molecules (External Reference) 

1 Unique

Entity ID: 5
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900003	G [auth E], H, I	sucrose	Oligosaccharide / Nutrient

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.28 Å
• R-Value Free:  0.224 (Depositor), 0.232 (DCC) 
• R-Value Work:  0.184 (Depositor), 0.199 (DCC) 
• R-Value Observed: 0.186 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 63.83	α = 90
b = 110.83	β = 90
c = 264.96	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-11-18 
Deposition Author(s): Scapin, G., Prosise, W., Reichert, P.

Revision History  

• Version 1.0: 2015-11-18
  Type: Initial release
  
• Version 1.1: 2016-07-06
  Changes: Database references
• Version 1.2: 2016-08-03
  Changes: Database references
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary
• Version 2.1: 2024-11-13
  Changes: Data collection, Database references, Derived calculations, Structure summary