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- PDB-8jh6: Crystal structure of apixaban-bound racemic ABLE -

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Basic information

Entry
Database: PDB / ID: 8jh6
TitleCrystal structure of apixaban-bound racemic ABLE
Components
  • D-ABLE
  • L-ABLE
KeywordsDE NOVO PROTEIN / Small molecule-binding protein / Racemic protein
Function / homologyChem-GG2 / polypeptide(D) / polypeptide(D) (> 10) / polypeptide(D) (> 100)
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsZhao, K. / Li, T.
Funding support China, 3items
OrganizationGrant numberCountry
Other private32120103013 China
Other governmentNo. 2021C03040 China
National Natural Science Foundation of China (NSFC)22077104 China
CitationJournal: Nat Biomed Eng / Year: 2025
Title: Rapid clearance of achiral small-molecule drugs using de novo-designed proteins and their cyclic and mirror-image variants
Authors: Zhao, K. / Li, T.
History
DepositionMay 22, 2023Deposition site: PDBJ / Processing site: PDBC
Revision 1.0May 29, 2024Provider: repository / Type: Initial release
Revision 1.1Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / Item: _pdbx_entry_details.has_protein_modification
Revision 1.2Jun 4, 2025Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: D-ABLE
B: L-ABLE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,5444
Polymers27,6252
Non-polymers9192
Water4,900272
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3580 Å2
ΔGint-7 kcal/mol
Surface area11920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)33.362, 42.483, 43.994
Angle α, β, γ (deg.)90.53, 97.91, 110.83
Int Tables number1
Space group name H-MP1

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Components

#1: Protein D-ABLE


Mass: 13807.421 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Protein L-ABLE


Mass: 13817.490 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)
#3: Chemical ChemComp-GG2 / 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


Mass: 459.497 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C25H25N5O4 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 272 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.09 Å3/Da / Density % sol: 41.02 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: 0.2 M Sodium sulfate decahydrate, 20% PEG 3350.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: Cu FINE FOCUS / Wavelength: 1.5418 Å
DetectorType: AGILENT ATLAS CCD / Detector: CCD / Date: Feb 4, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8→28.42 Å / Num. obs: 20692 / % possible obs: 96.9 % / Redundancy: 9.7 % / Biso Wilson estimate: 11.79 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.1038 / Net I/σ(I): 16.65
Reflection shellResolution: 1.8→1.864 Å / Rmerge(I) obs: 0.517 / Num. unique obs: 2084 / CC1/2: 0.941

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
CrysalisProdata reduction
PHASERphasing
CrysalisProdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→28.42 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 30.43 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2683 2002 9.98 %
Rwork0.2495 --
obs0.2514 20064 96.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.8→28.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1942 0 68 272 2282
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0182044
X-RAY DIFFRACTIONf_angle_d1.9062759
X-RAY DIFFRACTIONf_dihedral_angle_d24.863787
X-RAY DIFFRACTIONf_chiral_restr0.682301
X-RAY DIFFRACTIONf_plane_restr0.023365
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.850.35081600.28921354X-RAY DIFFRACTION100
1.85-1.890.49581020.42981121X-RAY DIFFRACTION84
1.89-1.950.35971610.34691316X-RAY DIFFRACTION99
1.95-2.010.30011270.28151309X-RAY DIFFRACTION99
2.01-2.090.22911700.22861349X-RAY DIFFRACTION100
2.09-2.170.26421330.23911325X-RAY DIFFRACTION100
2.17-2.270.38091340.31961208X-RAY DIFFRACTION91
2.27-2.390.27241400.2511190X-RAY DIFFRACTION90
2.39-2.540.24161450.22811337X-RAY DIFFRACTION100
2.54-2.730.26851410.25611337X-RAY DIFFRACTION100
2.73-3.010.24381560.23841304X-RAY DIFFRACTION100
3.01-3.440.24951430.22211331X-RAY DIFFRACTION100
3.44-4.330.21791400.19591270X-RAY DIFFRACTION95
4.33-28.420.21561500.21931311X-RAY DIFFRACTION99

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