8VFQ | pdb_00008vfq

De novo design apixaban-binding protein: apx1049

• PDB DOI: https://doi.org/10.2210/pdb8VFQ/pdb

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


• Deposited: 2023-12-21 Released: 2024-12-25 
• Deposition Author(s): Bera, A.K., Lee, G.R., Baker, D.
• Funding Organization(s): National Institutes of Health/National Institute on Aging (NIH/NIA), Howard Hughes Medical Institute (HHMI), Department of Defense (DOD, United States)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 
  0.323 (Depositor), 0.323 (DCC) 
• R-Value Work: 
  0.279 (Depositor), 0.279 (DCC) 
• R-Value Observed: 
  0.284 (Depositor) 

Starting Model: other

Literature

Small-molecule binding and sensing with a designed protein family

Lee, G.R., Bera, A.K., Baker, D.

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.

Macromolecule Content 

• Total Structure Weight: 26.83 kDa 
• Atom Count: 1,919 
• Modeled Residue Count: 225 
• Deposited Residue Count: 234 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
De novo designed apixaban-binding protein apx1049	A, B	117	synthetic construct	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GG2 (Subject of Investigation/LOI)	C [auth A], D [auth B]	1-(4-METHOXYPHENYL)-7-OXO-6-[4-(2-OXOPIPERIDIN-1-YL)PHENYL]-4,5,6,7-TETRAHYDRO-1H-PYRAZOLO[3,4-C]PYRIDINE-3-CARBOXAMIDE C25 H25 N5 O4 QNZCBYKSOIHPEH-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free:  0.323 (Depositor), 0.323 (DCC) 
• R-Value Work:  0.279 (Depositor), 0.279 (DCC) 
• R-Value Observed: 0.284 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 55.47	α = 90
b = 60.271	β = 90
c = 63.277	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-12-25 
Deposition Author(s): Bera, A.K., Lee, G.R., Baker, D.

---

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute on Aging (NIH/NIA)	United States	--
Howard Hughes Medical Institute (HHMI)	United States	--
Department of Defense (DOD, United States)	United States	--

Revision History  

• Version 1.0: 2024-12-25
  Type: Initial release