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- PDB-8fr4: Carbonic Anhydrase IX-mimic in complex with the alkyl urea compound 3j -

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Basic information

Entry
Database: PDB / ID: 8fr4
TitleCarbonic Anhydrase IX-mimic in complex with the alkyl urea compound 3j
ComponentsCarbonic anhydrase 2
KeywordsMETAL BINDING PROTEIN / Lyase / Inhibitor
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 / cyanamide hydratase activity / 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 / cyanamide hydratase activity / 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 / cytosol / cytoplasm
Similarity search - Function
Carbonic Anhydrase II / Alpha carbonic anhydrase / 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 ...Carbonic Anhydrase II / Alpha carbonic anhydrase / 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 / Roll / Alpha Beta
Similarity search - Domain/homology
Chem-N7S / Carbonic anhydrase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.123 Å
AuthorsCombs, J.E. / McKenna, R.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Molecules / Year: 2023
Title: New Insights into Conformationally Restricted Carbonic Anhydrase Inhibitors.
Authors: Combs, J. / Bozdag, M. / Cravey, L.D. / Kota, A. / McKenna, R. / Angeli, A. / Carta, F. / Supuran, C.T.
History
DepositionJan 6, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 1, 2023Provider: repository / Type: Initial release
Revision 1.1May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Carbonic anhydrase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,3054
Polymers28,8441
Non-polymers4613
Water3,747208
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)42.271, 41.433, 72.204
Angle α, β, γ (deg.)90.00, 103.60, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Carbonic anhydrase 2 / Carbonate dehydratase II / Carbonic anhydrase C / CAC / Carbonic anhydrase II / CA-II


Mass: 28844.465 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 / Production host: Escherichia coli (E. coli) / References: UniProt: P00918, carbonic anhydrase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-N7S / 4-hydroxy-3-{[(4-hydroxybutyl)carbamoyl]amino}benzene-1-sulfonamide


Mass: 303.335 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H17N3O5S / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 208 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.13 Å3/Da / Density % sol: 42.27 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.8 / Details: 1.6 M sodium citrate, 50 mM Tris base

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.9775 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 8, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9775 Å / Relative weight: 1
ReflectionResolution: 1.1→39.8 Å / Num. obs: 279296 / % possible obs: 92 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 10.9
Reflection shellResolution: 1.1→1.2 Å / Rmerge(I) obs: 0.76 / Num. unique obs: 19725

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.19refinement
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4zao

4zao


Resolution: 1.123→39.768 Å / SU ML: 0.09 / Cross valid method: NONE / σ(F): 1.33 / Phase error: 18.3 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1731 1977 2.3 %
Rwork0.1686 --
obs0.1687 85803 92.5 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.123→39.768 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2042 0 27 208 2277
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062150
X-RAY DIFFRACTIONf_angle_d0.8692923
X-RAY DIFFRACTIONf_dihedral_angle_d4.8411278
X-RAY DIFFRACTIONf_chiral_restr0.084303
X-RAY DIFFRACTIONf_plane_restr0.006379
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.123-1.15080.2166900.24493988X-RAY DIFFRACTION62
1.1508-1.18190.24231380.22495688X-RAY DIFFRACTION88
1.1819-1.21670.22331390.21515813X-RAY DIFFRACTION90
1.2167-1.2560.20461390.2155931X-RAY DIFFRACTION92
1.256-1.30090.23391420.20535936X-RAY DIFFRACTION93
1.3009-1.3530.19671450.18536177X-RAY DIFFRACTION95
1.353-1.41450.18471490.18566185X-RAY DIFFRACTION96
1.4145-1.48910.20421410.1836043X-RAY DIFFRACTION94
1.4891-1.58240.17661430.16776246X-RAY DIFFRACTION97
1.5824-1.70460.16211530.16186306X-RAY DIFFRACTION97
1.7046-1.87610.15591470.16146173X-RAY DIFFRACTION95
1.8761-2.14760.14821500.15926416X-RAY DIFFRACTION99
2.1476-2.70570.17531480.16666342X-RAY DIFFRACTION97
2.7057-39.70.16011530.15086582X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: -30.1728 Å / Origin y: -1.8829 Å / Origin z: 15.9681 Å
111213212223313233
T0.0708 Å20.0023 Å20.0022 Å2-0.0694 Å20.0002 Å2--0.0727 Å2
L0.5821 °2-0.0014 °20.0733 °2-0.5612 °20.0484 °2--0.5781 °2
S-0.0123 Å °-0.0039 Å °0.0141 Å °-0.0292 Å °0.0101 Å °-0.0109 Å °0.0069 Å °0.014 Å °0.0039 Å °
Refinement TLS groupSelection details: all

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