8VEZ | pdb_00008vez

De novo design apixaban-binding protein: apx1049

PDB DOI: https://doi.org/10.2210/pdb8VEZ/pdb

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

Deposited: 2023-12-20 Released: 2025-01-15
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: 2.15 Å
R-Value Free:
0.277 (Depositor), 0.277 (DCC)
R-Value Work:
0.223 (Depositor), 0.223 (DCC)
R-Value Observed:
0.228 (Depositor)

Starting Model: other
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Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

Small-molecule binding and sensing with a designed protein family

Lee, G.R., Bera, A.K., Baker, D.

To be published.

Macromolecule Content

Total Structure Weight: 13.56 kDa
Atom Count: 951
Modeled Residue Count: 115
Deposited Residue Count: 119
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
De novo design apixaban-binding protein: apx1049	A	119	synthetic construct	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GG2 (Subject of Investigation/LOI) Query on GG2 Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	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		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.15 Å
R-Value Free: 0.277 (Depositor), 0.277 (DCC)
R-Value Work: 0.223 (Depositor), 0.223 (DCC)
R-Value Observed: 0.228 (Depositor)

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 54.971	α = 90
b = 64.176	β = 90
c = 60.108	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2025-01-15

Deposition Author(s):

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 (Full details and data files)

Version 1.0: 2025-01-15
Type: Initial release

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.