7YDS | pdb_00007yds

The structure of the bispecific antibody targeted PD-L1 and 4-1BB

• PDB DOI: https://doi.org/10.2210/pdb7YDS/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Homo sapiens
• Expression System: Homo sapiens
• Mutation(s): Yes 


• Deposited: 2022-07-04 Released: 2023-07-19 
• Deposition Author(s): Gao, Y., Zhu, M., Liu, W.T., Cheng, L.S., Zhu, Z.L., Niu, L.W.
• Funding Organization(s): National Natural Science Foundation of China (NSFC), Ministry of Science and Technology (MoST, China)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 
  0.246 (Depositor), 0.246 (DCC) 
• R-Value Work: 
  0.194 (Depositor), 0.195 (DCC) 
• R-Value Observed: 
  0.197 (Depositor) 

Starting Models: experimental

Literature

A bispecific antibody targeted PD-L1 and 4-1BB induces a potent antitumor immune activity in colorectal cancer without systemic toxicity

Zhu, M., Gao, Y.

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 and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 64.19 kDa 
• Atom Count: 4,623 
• Modeled Residue Count: 551 
• Deposited Residue Count: 585 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Programmed cell death 1 ligand 1	A	147	Homo sapiens	Mutation(s): 1  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

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Anti-PDL1-VH-CH1	B	221	Homo sapiens	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Anti-PDL1-VL-CL	C	217	Homo sapiens	Mutation(s): 0

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free:  0.246 (Depositor), 0.246 (DCC) 
• R-Value Work:  0.194 (Depositor), 0.195 (DCC) 
• R-Value Observed: 0.197 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 71.076	α = 90
b = 94.88	β = 90
c = 96.069	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
autoPROC	data processing
Aimless	data scaling
MLPHARE	phasing
CrysalisPro	data reduction

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2023-07-19 
Deposition Author(s): Gao, Y., Zhu, M., Liu, W.T., Cheng, L.S., Zhu, Z.L., Niu, L.W.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	31621002
National Natural Science Foundation of China (NSFC)	China	92153302
Ministry of Science and Technology (MoST, China)	China	2017YFA0504903

Revision History  

• Version 1.0: 2023-07-19
  Type: Initial release
  
• Version 1.1: 2023-11-29
  Changes: Data collection, Refinement description
• Version 1.2: 2024-10-23
  Changes: Structure summary