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- PDB-6t81: Human Carbonic anhydrase II bound by 2-Naphthalenesulfonamide. -

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Basic information

Entry
Database: PDB / ID: 6t81
TitleHuman Carbonic anhydrase II bound by 2-Naphthalenesulfonamide.
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
AZIDE ION / naphthalene-2-sulfonamide / Carbonic anhydrase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 0.98 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 23, 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

Downloads & links

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Assembly

Deposited unit
A: carbonic anhydrase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,7906
Polymers29,2891
Non-polymers5015
Water5,657314
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area550 Å2
ΔGint-2 kcal/mol
Surface area11160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.032, 41.009, 71.684
Angle α, β, γ (deg.)90.000, 104.130, 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, 319 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-MUE / naphthalene-2-sulfonamide


Mass: 207.249 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H9NO2S / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-BCN / BICINE


Mass: 163.172 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4 / Comment: pH buffer*YM
#5: Chemical ChemComp-AZI / AZIDE ION


Mass: 42.020 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: N3
#6: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 314 / 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: 2.05 Å3/Da / Density % sol: 39.87 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.1M sodium bicine (pH 9) and 2M sodium malonate (pH 7)

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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: P14 (MX2) / Wavelength: 0.9768 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Dec 4, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9768 Å / Relative weight: 1
ReflectionResolution: 0.98→40.76 Å / Num. all: 114851 / Num. obs: 114851 / % possible obs: 84.8 % / Redundancy: 6.6 % / Rpim(I) all: 0.022 / Rrim(I) all: 0.056 / Rsym value: 0.042 / Net I/av σ(I): 4 / Net I/σ(I): 28.2 / Num. measured all: 754937
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
0.98-1.035.90.3172.365316111400.1550.3860.3175.656.7
1.03-1.160.1953.781333136490.0970.240.1958.773.3
1.1-1.175.90.116.685394143840.0570.1390.111481.8
1.17-1.266.70.0838.9100892150310.0410.1060.0831992.4
1.26-1.396.90.05912.596667140980.030.0790.05924.994
1.39-1.557.10.041891885129340.0220.0580.0433.494.7
1.55-1.797.10.0292381743115580.0170.0450.02943.796
1.79-2.1970.02425.16951399050.0130.0350.02454.297.2
2.19-3.16.80.02616.85297477860.0140.0350.02659.898.2
3.1-40.766.70.0528.72922043660.0260.0670.05263.198.2

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Processing

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

4ht0


Resolution: 0.98→39.64 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.964 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.029 / ESU R Free: 0.03
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1716 11479 10 %RANDOM
Rwork0.1456 ---
obs0.1482 103336 84.62 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å
Displacement parametersBiso max: 91.34 Å2 / Biso mean: 14.733 Å2 / Biso min: 5.1 Å2
Baniso -1Baniso -2Baniso -3
1-0.72 Å20 Å2-0.01 Å2
2---0.57 Å20 Å2
3----0.13 Å2
Refinement stepCycle: final / Resolution: 0.98→39.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2035 0 44 314 2393
Biso mean--16.96 26.46 -
Num. residues----258
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0122467
X-RAY DIFFRACTIONr_angle_refined_deg2.4041.6563388
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3385317
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.28623.306124
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.27915397
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.8841510
X-RAY DIFFRACTIONr_chiral_restr0.1520.2294
X-RAY DIFFRACTIONr_gen_planes_refined0.0160.022002
X-RAY DIFFRACTIONr_rigid_bond_restr12.39932467
X-RAY DIFFRACTIONr_sphericity_free22.4545142
X-RAY DIFFRACTIONr_sphericity_bonded13.23852546
LS refinement shellResolution: 0.98→1.005 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.208 479 -
Rwork0.195 4386 -
all-4865 -
obs--48.75 %

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