5E03 | pdb_00005e03

Crystal structure of mouse CTLA-4 nanobody

• PDB DOI: https://doi.org/10.2210/pdb5E03/pdb

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


• Deposited: 2015-09-28 Released: 2015-10-07 
• Deposition Author(s): Fedorov, A.A., Fedorov, E.V., Samanta, D., Bonanno, J.B., Almo, S.C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.69 Å
• R-Value Free: 
  0.189 (Depositor), 0.197 (DCC) 
• R-Value Work: 
  0.171 (Depositor), 0.182 (DCC) 
• R-Value Observed: 
  0.172 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of mouse CTLA-4 nanobody

Fedorov, A.A., Fedorov, E.V., Samanta, D., Bonanno, J.B., Almo, S.C.

To be published.

Biological Assembly 1  

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

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

Macromolecule Content 

• Total Structure Weight: 13.78 kDa 
• Atom Count: 961 
• Modeled Residue Count: 113 
• Deposited Residue Count: 129 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CTLA-4 nanobody	A	129	Camelidae	Mutation(s): 0

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.69 Å
• R-Value Free:  0.189 (Depositor), 0.197 (DCC) 
• R-Value Work:  0.171 (Depositor), 0.182 (DCC) 
• R-Value Observed: 0.172 (Depositor) 

Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.147	α = 90
b = 42.147	β = 90
c = 208.517	γ = 120

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-10-07 
Deposition Author(s): Fedorov, A.A., Fedorov, E.V., Samanta, D., Bonanno, J.B., Almo, S.C.

Revision History  

• Version 1.0: 2015-10-07
  Type: Initial release
  
• Version 1.1: 2015-10-14
  Changes: Database references, Structure summary
• Version 1.2: 2016-03-09
  Changes: Database references, Structure summary
• Version 1.3: 2017-11-22
  Changes: Derived calculations, Refinement description
• Version 1.4: 2019-01-30
  Changes: Data collection, Source and taxonomy, Structure summary
• Version 1.5: 2023-09-27
  Changes: Data collection, Database references, Refinement description
• Version 1.6: 2024-10-16
  Changes: Structure summary