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- PDB-6t5c: Human Carbonic anhydrase II bound by anthracene-9-sulfonamide -

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Basic information

Entry
Database: PDB / ID: 6t5c
TitleHuman Carbonic anhydrase II bound by anthracene-9-sulfonamide
Componentscarbonic anhydrase 2
KeywordsLYASE / drug design / carbonic anhydrase / benzenesulfonamide / metal-binding / lyase-lyase inhibitor complex
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
anthracene-9-sulfonamide / DI(HYDROXYETHYL)ETHER / Carbonic anhydrase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.22 Å
AuthorsSmirnov, A. / Manakova, E. / Grazulis, S.
CitationJournal: Biophys.J. / Year: 2020
Title: Isoform-Selective Enzyme Inhibitors by Exploring Pocket Size According to the Lock-and-Key Principle.
Authors: Dudutiene, V. / Zubriene, A. / Kairys, V. / Smirnov, A. / Smirnoviene, J. / Leitans, J. / Kazaks, A. / Tars, K. / Manakova, L. / Grazulis, S. / Matulis, D.
History
DepositionOct 15, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 14, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 28, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)30,0657
Polymers29,2891
Non-polymers7766
Water7,044391
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area850 Å2
ΔGint5 kcal/mol
Surface area11650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.309, 41.313, 71.971
Angle α, β, γ (deg.)90.000, 104.260, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 1 molecules A

#1: Protein carbonic anhydrase 2


Mass: 29289.062 Da / Num. of mol.: 1 / Fragment: Human Carbonic anhydrase II
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET15b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P00918, carbonic anhydrase

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Non-polymers , 6 types, 397 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-BCN / BICINE


Mass: 163.172 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4 / Comment: pH buffer*YM
#4: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#6: Chemical ChemComp-MJT / anthracene-9-sulfonamide


Mass: 257.308 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H11NO2S / Feature type: SUBJECT OF INVESTIGATION
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 391 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 40.98 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: Crystallization buffer was 0.1M sodium BICINE, pH 9, 0.2 M ammonium sulfate and 2M sodium malonate pH 7 made from 1M sodium BICINE and 3.4M sodium malonate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.9797 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jul 19, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9797 Å / Relative weight: 1
ReflectionResolution: 1.219→69.753 Å / Num. all: 68705 / Num. obs: 68705 / % possible obs: 95.7 % / Redundancy: 6.7 % / Rpim(I) all: 0.017 / Rrim(I) all: 0.044 / Rsym value: 0.035 / Net I/av σ(I): 7.4 / Net I/σ(I): 29.3 / Num. measured all: 459333
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique obsRpim(I) allRrim(I) allRsym valueNet I/σ(I) obs% possible all
1.22-1.295.90.0878.45001085040.0440.1120.08712.981.7
1.29-1.366.80.0759.76485695040.0360.0960.07516.796.3
1.36-1.466.70.05912.26004290030.030.0790.05919.997.1
1.46-1.576.90.04814.75807384310.0250.0650.04825.197.7
1.57-1.726.70.0417.25231678260.0210.0550.0430.298.2
1.72-1.9370.03618.54962871270.0180.0480.03636.998.7
1.93-2.236.70.03220.34255663190.0160.0420.03242.699.1
2.23-2.7370.03120.53770553890.0150.0390.0314799.7
2.73-3.866.70.0316.72846242260.0140.0370.0349.999.7
3.86-69.7536.60.03512.51568523760.0160.0420.03550.799.7

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Processing

Software
NameVersionClassification
SCALA3.3.20data scaling
REFMAC5.8.0232refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
MOLREPphasing
PDB_EXTRACTdata extraction
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4HT0

4ht0


Resolution: 1.22→69.75 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.971 / SU R Cruickshank DPI: 0.0422 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.042 / ESU R Free: 0.041
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1532 6954 10.1 %RANDOM
Rwork0.1228 ---
obs0.1259 61733 95.37 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å
Displacement parametersBiso max: 71.93 Å2 / Biso mean: 14.862 Å2 / Biso min: 5.43 Å2
Baniso -1Baniso -2Baniso -3
1-0.13 Å2-0 Å2-0.06 Å2
2---0.2 Å2-0 Å2
3---0.09 Å2
Refinement stepCycle: final / Resolution: 1.22→69.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2043 0 46 391 2480
Biso mean--25.4 27.64 -
Num. residues----258
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0122382
X-RAY DIFFRACTIONr_angle_refined_deg2.1341.653270
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0915305
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.48224.035114
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.2815375
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.006157
X-RAY DIFFRACTIONr_chiral_restr0.1340.2288
X-RAY DIFFRACTIONr_gen_planes_refined0.0190.021913
X-RAY DIFFRACTIONr_rigid_bond_restr7.6432382
X-RAY DIFFRACTIONr_sphericity_free21.335198
X-RAY DIFFRACTIONr_sphericity_bonded11.22652489
LS refinement shellResolution: 1.22→1.251 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.142 342 -
Rwork0.102 3261 -
obs--68.51 %

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