4N8P | pdb_00004n8p

Crystal structure of a strand swapped CTLA-4 from Duckbill Platypus [PSI-NYSGRC-012711]

• PDB DOI: https://doi.org/10.2210/pdb4N8P/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Ornithorhynchus anatinus
• Expression System: Trichoplusia ni
• Mutation(s): No 


• Deposited: 2013-10-17 Released: 2013-10-30 
• Deposition Author(s): Kumar, P.R., Banu, R., Bhosle, R., Calarese, D.A., Celikgil, A., Chamala, S., Chan, M.K., Chowdhury, S., Fiser, A., Garforth, S.J., Glenn, A.S., Hillerich, B., Khafizov, K., Attonito, J., Love, J.D., Patel, H., Patel, R., Seidel, R.D., Smith, B., Stead, M., Toro, R., Casadevall, A., Almo, S.C., New York Structural Genomics Research Consortium (NYSGRC), Atoms-to-Animals: The Immune Function Network (IFN)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 
  0.212 (Depositor), 0.214 (DCC) 
• R-Value Work: 
  0.173 (Depositor), 0.189 (DCC) 
• R-Value Observed: 
  0.175 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of a strand swapped CTLA-4 from Duckbill Platypus [PSI-NYSGRC-012711]

Kumar, P.R., Casadevall, A., 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: 15.57 kDa 
• Atom Count: 1,005 
• Modeled Residue Count: 119 
• Deposited Residue Count: 135 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Uncharacterized protein	A	135	Ornithorhynchus anatinus	Mutation(s): 0  Gene Names: CTLA-4, CTLA4
UniProt
Find proteins for F6ZMI5 (Ornithorhynchus anatinus) Explore F6ZMI5  Go to UniProtKB:  F6ZMI5

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	C [auth A], D [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
GOL	B [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free:  0.212 (Depositor), 0.214 (DCC) 
• R-Value Work:  0.173 (Depositor), 0.189 (DCC) 
• R-Value Observed: 0.175 (Depositor) 

Space Group: I 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 37.272	α = 90
b = 107.991	β = 90
c = 109.723	γ = 90

Software Package:

Software Name	Purpose
SCALA	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
CBASS	data collection
MOSFLM	data reduction
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-10-30 
Deposition Author(s): Kumar, P.R., Banu, R., Bhosle, R., Calarese, D.A., Celikgil, A., Chamala, S., Chan, M.K., Chowdhury, S., Fiser, A., Garforth, S.J., Glenn, A.S., Hillerich, B., Khafizov, K., Attonito, J., Love, J.D., Patel, H., Patel, R., Seidel, R.D., Smith, B., Stead, M., Toro, R., Casadevall, A., Almo, S.C., New York Structural Genomics Research Consortium (NYSGRC), Atoms-to-Animals: The Immune Function Network (IFN)

Revision History  

• Version 1.0: 2013-10-30
  Type: Initial release
  
• Version 1.1: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Database references, Derived calculations, Structure summary
• Version 1.2: 2023-09-20
  Changes: Data collection, Database references, Refinement description, Structure summary
• Version 1.3: 2024-11-20
  Changes: Structure summary