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- PDB-9oaf: Room temperature structure of human carbonic anhydrase IX mimic i... -

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Basic information

Entry
Database: PDB / ID: 9oaf
TitleRoom temperature structure of human carbonic anhydrase IX mimic in complex with vorinostat (drug soak)
ComponentsCarbonic anhydrase 2
KeywordsLYASE / Carbonic Anhydrase / Inhibitor Complex / Zinc Binding Protein
Function / homology
Function and homology information


positive regulation of cellular pH reduction / positive regulation of dipeptide transmembrane transport / regulation of monoatomic anion transport / secretion / cyanamide hydratase activity / cyanamide hydratase / arylesterase activity / regulation of chloride transport / Reversible hydration of carbon dioxide / morphogenesis of an epithelium ...positive regulation of cellular pH reduction / positive regulation of dipeptide transmembrane transport / regulation of monoatomic anion transport / secretion / cyanamide hydratase activity / cyanamide hydratase / arylesterase activity / regulation of chloride transport / Reversible hydration of carbon dioxide / morphogenesis of an epithelium / angiotensin-activated signaling pathway / positive regulation of synaptic transmission, GABAergic / regulation of intracellular pH / carbonic anhydrase / carbonate dehydratase activity / carbon dioxide transport / Erythrocytes take up oxygen and release carbon dioxide / Erythrocytes take up carbon dioxide and release oxygen / neuron cellular homeostasis / apical part of cell / myelin sheath / extracellular exosome / zinc ion binding / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Carbonic anhydrase, alpha-class, conserved site / Alpha-carbonic anhydrases signature. / Carbonic anhydrase, alpha-class / Alpha carbonic anhydrase domain / Alpha carbonic anhydrase domain superfamily / Eukaryotic-type carbonic anhydrase / Alpha-carbonic anhydrases profile. / Eukaryotic-type carbonic anhydrase
Similarity search - Domain/homology
OCTANEDIOIC ACID HYDROXYAMIDE PHENYLAMIDE / Carbonic anhydrase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsGulkis, M.C. / McKenna, R. / Fisher, S.Z.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2025
Title: Off-target binding of the histone deacetylase inhibitor vorinostat to carbonic anhydrase II and IX.
Authors: Gulkis, M.C. / Hodgkinson, J.T. / Sele, C.P. / Knecht, W. / McKenna, R. / Fisher, S.Z.
History
DepositionApr 21, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 8, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Carbonic anhydrase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,5313
Polymers29,2011
Non-polymers3302
Water4,017223
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)42.579, 41.671, 72.582
Angle α, β, γ (deg.)90.000, 104.012, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein Carbonic anhydrase 2 / Carbonate dehydratase II / Carbonic anhydrase C / CAC / Carbonic anhydrase II / CA-II / Cyanamide ...Carbonate dehydratase II / Carbonic anhydrase C / CAC / Carbonic anhydrase II / CA-II / Cyanamide hydratase CA2


Mass: 29200.887 Da / Num. of mol.: 1 / Mutation: A65S, N67Q, E69T, I91L, F131V, K170E, L204A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CA2 / Plasmid: pET26b / Production host: Escherichia coli (E. coli) / Strain (production host): TUNER (DE3)
References: UniProt: P00918, carbonic anhydrase, cyanamide hydratase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-SHH / OCTANEDIOIC ACID HYDROXYAMIDE PHENYLAMIDE / SAHA


Mass: 264.320 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H20N2O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 223 / 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: 2.14 Å3/Da / Density % sol: 42.51 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 50 mM Tris HCl pH 8.0, 1.25 M sodium citrate / Temp details: Room temperature

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Data collection

DiffractionMean temperature: 293 K / Ambient temp details: Room temperature / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: MAX IV / Beamline: BioMAX / Wavelength: 0.7293 Å
DetectorType: DECTRIS EIGER2 X CdTe 16M / Detector: PIXEL / Date: Dec 5, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.7293 Å / Relative weight: 1
ReflectionResolution: 1.4→24.73 Å / Num. obs: 48869 / % possible obs: 96.2 % / Redundancy: 3.3 % / Biso Wilson estimate: 15.18 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.065 / Rpim(I) all: 0.042 / Net I/σ(I): 10.4
Reflection shellResolution: 1.4→1.45 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.527 / Mean I/σ(I) obs: 2.5 / Num. unique obs: 3712 / CC1/2: 0.687 / Rpim(I) all: 0.35 / % possible all: 76.9

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Processing

Software
NameVersionClassification
PHENIX1.21_5207refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.4→22.93 Å / SU ML: 0.1301 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 18.5035
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.174 3749 4.24 %
Rwork0.1542 84738 -
obs0.155 47017 92.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 23.86 Å2
Refinement stepCycle: LAST / Resolution: 1.4→22.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2052 0 20 223 2295
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0122262
X-RAY DIFFRACTIONf_angle_d1.30943090
X-RAY DIFFRACTIONf_chiral_restr0.1006329
X-RAY DIFFRACTIONf_plane_restr0.0145402
X-RAY DIFFRACTIONf_dihedral_angle_d14.2196839
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4-1.420.29821020.27112250X-RAY DIFFRACTION66.25
1.42-1.440.23421260.2742332X-RAY DIFFRACTION70.05
1.44-1.460.2435990.26172701X-RAY DIFFRACTION79.32
1.46-1.480.28891670.26172905X-RAY DIFFRACTION87.92
1.48-1.50.2091250.24673229X-RAY DIFFRACTION94.85
1.5-1.520.26411500.23073209X-RAY DIFFRACTION94.81
1.52-1.550.23871290.22493199X-RAY DIFFRACTION95.09
1.55-1.570.24551390.20713211X-RAY DIFFRACTION94.85
1.57-1.60.1961390.20623251X-RAY DIFFRACTION95.17
1.6-1.630.22291420.18463203X-RAY DIFFRACTION95.22
1.63-1.670.20611310.19083261X-RAY DIFFRACTION95.28
1.67-1.70.21221430.18513204X-RAY DIFFRACTION94.76
1.7-1.740.19611540.16943219X-RAY DIFFRACTION95.58
1.74-1.790.19321080.16853245X-RAY DIFFRACTION95.26
1.79-1.830.1911510.16853169X-RAY DIFFRACTION95.16
1.83-1.890.18031580.15823273X-RAY DIFFRACTION96.03
1.89-1.950.20611400.16083256X-RAY DIFFRACTION96.83
1.95-2.020.15771430.14393279X-RAY DIFFRACTION96.42
2.02-2.10.16651500.14833219X-RAY DIFFRACTION95.96
2.1-2.20.17881380.1443316X-RAY DIFFRACTION96.89
2.2-2.310.20411490.14473228X-RAY DIFFRACTION95.48
2.31-2.460.20931420.15353221X-RAY DIFFRACTION96.2
2.46-2.640.19031470.15523269X-RAY DIFFRACTION96.44
2.64-2.910.17241510.15383220X-RAY DIFFRACTION95.9
2.91-3.330.15051380.14123303X-RAY DIFFRACTION97.42
3.33-4.190.1341380.11763326X-RAY DIFFRACTION97.36
4.19-22.930.11811500.12143240X-RAY DIFFRACTION96.12

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