13FL | pdb_000013fl

Structure of FabS1CE2_P2a in complex with the N-terminal domain of PD-L1

• PDB DOI: https://doi.org/10.2210/pdb13FL/pdb

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


• Deposited: 2026-05-04 Released: 2026-06-03 
• Deposition Author(s): Mallette, E., Singer, A.U., Blazer, L.L., Adams, J.J., Suits, M.D.L., Sidhu, S.S.
• Funding Organization(s): Canadian Institutes of Health Research (CIHR)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.22 Å
• R-Value Free: 
  0.239 (Depositor), 0.239 (DCC) 
• R-Value Work: 
  0.199 (Depositor), 0.200 (DCC) 
• R-Value Observed: 
  0.201 (Depositor) 

Starting Models: experimental

Literature

A Strategy for Modular Assembly of Tetravalent Multispecific Antibodies

Mallette, E., Blazer, L.L., Hokanson, C.A., Chen, C., Perez, J.G., Pavkenco, A., Ploder, L., Singer, A.U., Suits, M.D.L., Adams, J.J., Sidhu, S.S.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 3-mer - A2B1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 62.5 kDa 
• Atom Count: 4,316 
• Modeled Residue Count: 545 
• Deposited Residue Count: 565 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
FabS1CE2_P2a heavy chain	A	227	Homo sapiens	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
FabS1CE2_P2a light chain (Trastuzumab Fab Light Chain)	B	212	Homo sapiens	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Programmed cell death 1 ligand 1	C	126	Homo sapiens	Mutation(s): 0  Gene Names: CD274, B7H1, PDCD1L1, PDCD1LG1, PDL1
UniProt & NIH Common Fund Data Resources
Find proteins for Q9NZQ7 (Homo sapiens) Explore Q9NZQ7  Go to UniProtKB:  Q9NZQ7
PHAROS:  Q9NZQ7 GTEx:  ENSG00000120217
Glycosylation
Glycosylation Sites: 1		Go to GlyGen: Q9NZQ7-1

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	G [auth C]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
EDO	D [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
CL	E [auth A], F [auth B], H [auth C]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.22 Å
• R-Value Free:  0.239 (Depositor), 0.239 (DCC) 
• R-Value Work:  0.199 (Depositor), 0.200 (DCC) 
• R-Value Observed: 0.201 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 66.358	α = 90
b = 239.679	β = 90
c = 104.282	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PHENIX	refinement
autoPROC	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2026-06-03 
Deposition Author(s): Mallette, E., Singer, A.U., Blazer, L.L., Adams, J.J., Suits, M.D.L., Sidhu, S.S.

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Funding Organization	Location	Grant Number
Canadian Institutes of Health Research (CIHR)	Canada	MOP-93725
Canadian Institutes of Health Research (CIHR)	Canada	MOP-136944

Revision History  

• Version 1.0: 2026-06-03
  Type: Initial release