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- PDB-6t4p: Human Carbonic anhydrase II bound by napthalene-1-sulfonamide -

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Basic information

Entry
Database: PDB / ID: 6t4p
TitleHuman Carbonic anhydrase II bound by napthalene-1-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 / cyanamide hydratase activity / arylesterase activity / regulation of chloride transport / Reversible hydration of carbon dioxide / angiotensin-activated signaling pathway ...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 / angiotensin-activated signaling pathway / positive regulation of synaptic transmission, GABAergic / regulation of intracellular pH / morphogenesis of an epithelium / 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
naphthalene-1-sulfonamide / Carbonic anhydrase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 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 14, 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)29,9367
Polymers29,2891
Non-polymers6476
Water4,450247
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area880 Å2
ΔGint4 kcal/mol
Surface area11120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.072, 41.159, 71.704
Angle α, β, γ (deg.)90.000, 104.080, 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, 253 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE / Dimethyl sulfoxide


Mass: 78.133 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#4: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID / MES (buffer)


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#5: Chemical ChemComp-MHK / naphthalene-1-sulfonamide


Mass: 207.249 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H9NO2S / Feature type: SUBJECT OF INVESTIGATION
#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 / Water


Mass: 18.015 Da / Num. of mol.: 247 / 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: 2.06 Å3/Da / Density % sol: 40.17 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: Crystallization buffer was 0.1M sodium BICINE, pH 9, 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: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.815 Å
DetectorType: MAR555 FLAT PANEL / Detector: IMAGE PLATE / Date: Nov 19, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.815 Å / Relative weight: 1
ReflectionResolution: 1.75→31.96 Å / Num. all: 23997 / Num. obs: 23997 / % possible obs: 98.9 % / Redundancy: 6.8 % / Rmerge(I) obs: 0.071 / Rpim(I) all: 0.031 / Rrim(I) all: 0.081 / Rsym value: 0.071 / Net I/av σ(I): 7.3 / Net I/σ(I): 23.3 / Num. measured all: 163532
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
1.75-1.845.40.1155.31910835080.0580.140.1158.699.6
1.84-1.966.30.0996.22105433280.0450.1160.09913.6100
1.96-2.097.40.0926.52308431250.0380.1040.09219.4100
2.09-2.267.40.087.62169229140.0330.0910.0823.7100
2.26-2.477.40.0728.62016327080.030.0820.07227.1100
2.47-2.777.50.0688.81818224390.0280.0770.06830.5100
2.77-3.27.40.0659.11594521540.0280.0750.06534.4100
3.2-3.9170.0659.91271018190.0290.0740.06536.298.9
3.91-5.536.10.06210.6801613210.0290.0710.06234.192.7
5.53-31.965.30.0669.335786810.0340.0760.06631.483.2

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALA3.2.19data scaling
REFMAC5.8.0232refinement
PDB_EXTRACT3.25data extraction
MOLREPphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4HT0

4ht0


Resolution: 1.75→26.57 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.942 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.128 / ESU R Free: 0.119
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1993 2367 9.9 %RANDOM
Rwork0.1615 ---
obs0.1652 21618 98.76 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å
Displacement parametersBiso max: 62.89 Å2 / Biso mean: 16.051 Å2 / Biso min: 4.84 Å2
Baniso -1Baniso -2Baniso -3
1--0.09 Å2-0 Å2-0.35 Å2
2---0.25 Å20 Å2
3---0.46 Å2
Refinement stepCycle: final / Resolution: 1.75→26.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2036 0 32 247 2315
Biso mean--21.77 27.14 -
Num. residues----257
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0122151
X-RAY DIFFRACTIONr_angle_refined_deg1.8491.6432925
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0425261
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.08623.714105
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.93615344
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.508157
X-RAY DIFFRACTIONr_chiral_restr0.1330.2260
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.021673
LS refinement shellResolution: 1.75→1.795 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.295 177 -
Rwork0.231 1579 -
all-1756 -
obs--98.87 %

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