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- PDB-8vez: De novo design apixaban-binding protein: apx1049 -

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Basic information

Entry
Database: PDB / ID: 8vez
TitleDe novo design apixaban-binding protein: apx1049
ComponentsDe novo design apixaban-binding protein: apx1049
KeywordsDE NOVO PROTEIN / protein design / deep learning / small-molecule-binding / de novo design / apixaban
Function / homologyChem-GG2
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsBera, A.K. / Lee, G.R. / Baker, D.
Funding support United States, 3items
OrganizationGrant numberCountry
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
CitationJournal: To Be Published
Title: Small-molecule binding and sensing with a designed protein family
Authors: Lee, G.R. / Bera, A.K. / Baker, D.
History
DepositionDec 20, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 15, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: De novo design apixaban-binding protein: apx1049
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,5582
Polymers13,0981
Non-polymers4591
Water36020
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)54.971, 64.176, 60.108
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2

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Components

#1: Protein De novo design apixaban-binding protein: apx1049


Mass: 13098.239 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)
#2: 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.: 1 / Source method: obtained synthetically / Formula: C25H25N5O4 / Feature type: SUBJECT OF INVESTIGATION / Comment: medication, anticoagulant*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 20 / 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: 2.03 Å3/Da / Density % sol: 39.22 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1 M potassium thiocyanate and 30% PEG 2000 MME

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1.00009 Å
DetectorType: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: Dec 15, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00009 Å / Relative weight: 1
ReflectionResolution: 2.15→41.75 Å / Num. obs: 6020 / % possible obs: 99.7 % / Redundancy: 9.8 % / Biso Wilson estimate: 47.4 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.221 / Rpim(I) all: 0.075 / Net I/σ(I): 6.67
Reflection shellResolution: 2.15→2.37 Å / Redundancy: 9.6 % / Rmerge(I) obs: 2.419 / Mean I/σ(I) obs: 0.91 / Num. unique obs: 1474 / CC1/2: 0.46 / Rpim(I) all: 0.816 / % possible all: 99.53

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Processing

Software
NameVersionClassification
PHENIXdev_4761refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.15→41.75 Å / SU ML: 0.3136 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 34.7164
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2774 603 10.02 %
Rwork0.2229 5417 -
obs0.228 6020 99.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 55.38 Å2
Refinement stepCycle: LAST / Resolution: 2.15→41.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms897 0 34 20 951
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.002947
X-RAY DIFFRACTIONf_angle_d0.69081277
X-RAY DIFFRACTIONf_chiral_restr0.0456145
X-RAY DIFFRACTIONf_plane_restr0.0021156
X-RAY DIFFRACTIONf_dihedral_angle_d6.1092135
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.15-2.370.36271480.3281326X-RAY DIFFRACTION99.53
2.37-2.710.35731470.28541328X-RAY DIFFRACTION99.59
2.71-3.410.29991500.24291341X-RAY DIFFRACTION99.87
3.41-41.750.24361580.19141422X-RAY DIFFRACTION99.81
Refinement TLS params.Method: refined / Origin x: 12.1271201617 Å / Origin y: 15.2716190389 Å / Origin z: -5.9767874216 Å
111213212223313233
T0.351119229523 Å2-0.046812469952 Å20.0174445853256 Å2-0.328496879202 Å20.00140199366816 Å2--0.321852996124 Å2
L1.75448016404 °2-1.14688109392 °2-0.632700150036 °2-0.749538133251 °20.295786896783 °2--1.42219770186 °2
S-0.141532488683 Å °0.182093708024 Å °-0.0951547159201 Å °-0.00183255791125 Å °0.00819835765149 Å °0.0819702783661 Å °0.252762579016 Å °-0.246315685122 Å °-5.61185325223E-5 Å °
Refinement TLS groupSelection details: all

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