8PF0

Diubiquitin-derived artificial binding protein (Affilin) variant Af1 specific to oncofetal fibronectin

• PDB DOI: https://doi.org/10.2210/pdb8PF0/pdb

• Classification: DE NOVO PROTEIN
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2023-06-15 Released: 2024-06-26 
• Deposition Author(s): Parthier, C., Katzschmann, A., Fiedler, E., Haupts, U., Reimann, A.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.226 
• R-Value Work: 0.193 
• R-Value Observed: 0.195 

Literature

Ubiquitin-derived artificial binding proteins targeting oncofetal fibronectin reveal scaffold plasticity by beta-strand slippage

Katzschmann, A., Fiedler, E., Haupts, U., Reimann, A., Settele, F., Gloser-Braeunig, M., Parthier, C.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 17.92 kDa 
• Atom Count: 1,315 
• Modelled Residue Count: 153 
• Deposited Residue Count: 155 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Affilin variant Af1 (77405)	A	155	Homo sapiens	Mutation(s): 0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
IMD	F [auth A], G [auth A]	IMIDAZOLE C3 H5 N2 RAXXELZNTBOGNW-UHFFFAOYSA-O
CU	B [auth A], C [auth A], D [auth A], E [auth A]	COPPER (II) ION Cu JPVYNHNXODAKFH-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.226 
• R-Value Work: 0.193 
• R-Value Observed: 0.195 
• Space Group: P 4₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 62.767	α = 90
b = 62.767	β = 90
c = 67.841	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XSCALE	data scaling
XDS	data reduction
SHARP	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-06-26 
Deposition Author(s): Parthier, C., Katzschmann, A., Fiedler, E., Haupts, U., Reimann, A.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2024-06-26
  Type: Initial release