5DXW | pdb_00005dxw

Crystal structure of mouse PD-L1 nanobody

• PDB DOI: https://doi.org/10.2210/pdb5DXW/pdb

• Classification: SIGNALING PROTEIN
• Organism(s): Camelidae
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2015-09-24 Released: 2015-10-07 
• Deposition Author(s): Fedorov, A.A., Fedorov, E.V., Samanta, D., Almo, S.C., Ploegh, H., Ingram, J., Dougan, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.44 Å
• R-Value Free: 
  0.193 (Depositor), 0.196 (DCC) 
• R-Value Work: 
  0.169 (Depositor), 0.169 (DCC) 
• R-Value Observed: 
  0.170 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of mouse PD-L1 nanobody

Fedorov, A.A., Fedorov, E.V., Samanta, D., Almo, S.C.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly 3  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 3 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 14.54 kDa 
• Atom Count: 1,012 
• Modeled Residue Count: 114 
• Deposited Residue Count: 130 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PD-L1 nanobody	A	130	Camelidae	Mutation(s): 0

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.44 Å
• R-Value Free:  0.193 (Depositor), 0.196 (DCC) 
• R-Value Work:  0.169 (Depositor), 0.169 (DCC) 
• R-Value Observed: 0.170 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 85.191	α = 90
b = 29.679	β = 90
c = 35.268	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
CBASS	data collection
HKL-2000	data reduction
PHASER	phasing
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-10-07 
Deposition Author(s): Fedorov, A.A., Fedorov, E.V., Samanta, D., Almo, S.C., Ploegh, H., Ingram, J., Dougan, M.

Revision History  

• Version 1.0: 2015-10-07
  Type: Initial release
  
• Version 1.1: 2016-03-02
  Changes: Structure summary
• Version 1.2: 2019-01-30
  Changes: Data collection, Derived calculations, Source and taxonomy, Structure summary
• Version 1.3: 2023-09-27
  Changes: Data collection, Database references, Refinement description
• Version 1.4: 2024-10-23
  Changes: Structure summary