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- PDB-7oym: Carbonic anhydrase II in complex with Hit2 (MH65) -

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Basic information

Entry
Database: PDB / ID: 7oym
TitleCarbonic anhydrase II in complex with Hit2 (MH65)
Components
  • Carbonic anhydrase 2
  • Hit2 (MH65)
KeywordsLYASE / carbonic anhydrase / 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 / regulation of chloride transport / arylesterase activity / Reversible hydration of carbon dioxide / positive regulation of synaptic transmission, GABAergic ...positive regulation of cellular pH reduction / positive regulation of dipeptide transmembrane transport / regulation of monoatomic anion transport / secretion / cyanamide hydratase / cyanamide hydratase activity / regulation of chloride transport / arylesterase activity / Reversible hydration of carbon dioxide / positive regulation of synaptic transmission, GABAergic / angiotensin-activated signaling pathway / morphogenesis of an epithelium / 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 / one-carbon metabolic process / apical part of cell / myelin sheath / extracellular exosome / zinc ion binding / plasma membrane / cytosol / cytoplasm
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
Carbonic anhydrase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 0.98 Å
AuthorsKugler, M. / Brynda, J. / Rezacova, P.
CitationJournal: Rsc Med Chem / Year: 2023
Title: Identification of specific carbonic anhydrase inhibitors via in situ click chemistry, phage-display and synthetic peptide libraries: comparison of the methods and structural study.
Authors: Kugler, M. / Hadzima, M. / Dzijak, R. / Rampmaier, R. / Srb, P. / Vrzal, L. / Voburka, Z. / Majer, P. / Rezacova, P. / Vrabel, M.
History
DepositionJun 24, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 18, 2023Provider: repository / Type: Initial release
Revision 1.1Feb 22, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Carbonic anhydrase 2
B: Hit2 (MH65)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,4213
Polymers30,3552
Non-polymers651
Water5,837324
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area840 Å2
ΔGint-43 kcal/mol
Surface area11510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.260, 41.270, 72.300
Angle α, β, γ (deg.)90.000, 104.440, 90.000
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: 29289.062 Da / Num. of mol.: 1
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: Protein/peptide Hit2 (MH65)


Mass: 1066.169 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 324 / 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: 2.08 Å3/Da / Density % sol: 41 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.8 / Details: 1.6 M sodium citrate, 50 mM Tris-H2SO4

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 12, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 0.98→40.93 Å / Num. obs: 122587 / % possible obs: 93.8 % / Redundancy: 3.542 % / Biso Wilson estimate: 13.223 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.048 / Rrim(I) all: 0.056 / Χ2: 0.853 / Net I/σ(I): 12.57
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
1-1.062.7560.4811.774099821024148750.7990.58870.8
1.06-1.133.4490.2623.886696919750194170.9280.31198.3
1.13-1.223.5030.1566.446283318419179380.9720.18497.4
1.22-1.343.7350.1089.576271916973167910.9860.12698.9
1.34-1.53.7890.07513.645735315340151380.9920.08898.7
1.5-1.733.5810.05418.814742313590132430.9950.06397.4
1.73-2.123.90.04425.824461911546114400.9970.05199.1
2.12-2.993.5920.04128.4331352893487280.9960.04897.7
2.99-40.933.9670.04132.719900504850170.9970.04799.4

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
REFMAC5.8.0257refinement
PDB_EXTRACT3.27data extraction
FFTphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 3PO6

3po6


Resolution: 0.98→40.93 Å / Cor.coef. Fo:Fc: 0.982 / Cor.coef. Fo:Fc free: 0.974 / SU B: 0.693 / SU ML: 0.016 / SU R Cruickshank DPI: 0.022 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.022 / ESU R Free: 0.023 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1602 2498 2 %RANDOM
Rwork0.1356 ---
obs0.136 122362 89.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 125.14 Å2 / Biso mean: 16.823 Å2 / Biso min: 8.39 Å2
Baniso -1Baniso -2Baniso -3
1-0.28 Å2-0 Å2-0.14 Å2
2---0.2 Å2-0 Å2
3----0.01 Å2
Refinement stepCycle: final / Resolution: 0.98→40.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2030 0 35 347 2412
Biso mean--37.6 29.77 -
Num. residues----257
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0132249
X-RAY DIFFRACTIONr_bond_other_d0.0020.0172019
X-RAY DIFFRACTIONr_angle_refined_deg1.7651.6413080
X-RAY DIFFRACTIONr_angle_other_deg1.5271.5844735
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.125285
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.92924110
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.07215368
X-RAY DIFFRACTIONr_dihedral_angle_4_deg25.608157
X-RAY DIFFRACTIONr_chiral_restr0.10.2276
X-RAY DIFFRACTIONr_gen_planes_refined0.010.022559
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02459
X-RAY DIFFRACTIONr_rigid_bond_restr16.95234267
LS refinement shellResolution: 0.98→1.004 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.331 59 -
Rwork0.322 2859 -
obs--28.47 %

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