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- PDB-6rh4: Human Carbonic Anhydrase II in complex with 4-Nitrobenzenesulfonamide. -

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Basic information

Entry
Database: PDB / ID: 6rh4
TitleHuman Carbonic Anhydrase II in complex with 4-Nitrobenzenesulfonamide.
ComponentsCarbonic anhydrase 2
KeywordsLYASE / Inihibitor / complex / CO2 conversion
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 / regulation of intracellular pH / positive regulation of synaptic transmission, GABAergic / 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
4-nitrobenzenesulfonamide / (4-CARBOXYPHENYL)(CHLORO)MERCURY / beta-D-glucopyranose / alpha-D-glucopyranose / : / Carbonic anhydrase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 0.948 Å
AuthorsGloeckner, S. / Heine, A. / Klebe, G.
CitationJournal: Biomolecules / Year: 2020
Title: The Influence of Varying Fluorination Patterns on the Thermodynamics and Kinetics of Benzenesulfonamide Binding to Human Carbonic Anhydrase II.
Authors: Glockner, S. / Ngo, K. / Wagner, B. / Heine, A. / Klebe, G.
History
DepositionApr 18, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 15, 2020Provider: repository / Type: Initial release
Revision 1.1Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _entity.pdbx_description ..._chem_comp.name / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_comp_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.2Jan 24, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _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)31,3759
Polymers29,8071
Non-polymers1,5688
Water4,486249
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1180 Å2
ΔGint-23 kcal/mol
Surface area11460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.438, 41.522, 72.273
Angle α, β, γ (deg.)90.00, 104.74, 90.00
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 / Carbonate dehydratase II / Carbonic anhydrase C / CAC / Carbonic anhydrase II / CA-II


Mass: 29806.588 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: The first 5 amino acids (GSPEF) are remnants of an expression tag.
Source: (gene. exp.) Homo sapiens (human) / Gene: CA2 / Plasmid: pGEX-4T1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Codon plus / References: UniProt: P00918, carbonic anhydrase

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Sugars , 2 types, 3 molecules

#5: Sugar ChemComp-BGC / beta-D-glucopyranose / beta-D-glucose / D-glucose / glucose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DGlcpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-glucopyranoseCOMMON NAMEGMML 1.0
b-D-GlcpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#6: Sugar ChemComp-GLC / alpha-D-glucopyranose / alpha-D-glucose / D-glucose / glucose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DGlcpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-glucopyranoseCOMMON NAMEGMML 1.0
a-D-GlcpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 5 types, 254 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-HG / MERCURY (II) ION


Mass: 200.590 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Hg
#4: Chemical ChemComp-BE7 / (4-CARBOXYPHENYL)(CHLORO)MERCURY / P-CHLOROMERCURIBENZOIC ACID


Mass: 357.156 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H5ClHgO2
#7: Chemical ChemComp-4NZ / 4-nitrobenzenesulfonamide


Mass: 202.188 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H6N2O4S
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 249 / Source method: isolated from a natural source / Formula: H2O

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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: 2.07 Å3/Da / Density % sol: 40.77 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.8
Details: Ammonium sulfate 2.40 M, TRIS 0.1 M, pH = 7.8, saturated with para-Chloromercuribenzoic acid

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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 PILATUS 6M / Detector: PIXEL / Date: Apr 8, 2018 / Details: Sagitally bended Si(111) crystal
RadiationMonochromator: Double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 0.948→41.522 Å / Num. obs: 148154 / % possible obs: 96.3 % / Redundancy: 3.5 % / Biso Wilson estimate: 6.8 Å2 / CC1/2: 0.998 / Rsym value: 0.053 / Net I/σ(I): 12.65
Reflection shellResolution: 0.95→1.01 Å / Redundancy: 3.16 % / Mean I/σ(I) obs: 3.25 / Num. unique obs: 22694 / CC1/2: 0.909 / Rsym value: 0.254 / % possible all: 91.5

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3KS3

3ks3


Resolution: 0.948→41.042 Å / SU ML: 0.05 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 7.9
RfactorNum. reflection% reflectionSelection details
Rfree0.117 7408 5 %Random selection of 5 %
Rwork0.1029 ---
obs0.1036 148150 96.36 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 0.948→41.042 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2023 0 74 249 2346
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082563
X-RAY DIFFRACTIONf_angle_d1.073541
X-RAY DIFFRACTIONf_dihedral_angle_d14.683974
X-RAY DIFFRACTIONf_chiral_restr0.087367
X-RAY DIFFRACTIONf_plane_restr0.009494
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
0.9485-0.95930.17011950.16733708X-RAY DIFFRACTION76
0.9593-0.97060.15112410.14184586X-RAY DIFFRACTION95
0.9706-0.98240.13972450.13154655X-RAY DIFFRACTION96
0.9824-0.99480.13432430.11944612X-RAY DIFFRACTION96
0.9948-1.00790.13142450.10884647X-RAY DIFFRACTION95
1.0079-1.02170.11042410.10464581X-RAY DIFFRACTION95
1.0217-1.03630.11962430.10634621X-RAY DIFFRACTION94
1.0363-1.05180.11562440.09864627X-RAY DIFFRACTION97
1.0518-1.06820.10692520.08774804X-RAY DIFFRACTION98
1.0682-1.08570.10072520.07944787X-RAY DIFFRACTION98
1.0857-1.10450.09322490.0814714X-RAY DIFFRACTION98
1.1045-1.12460.0892510.07594787X-RAY DIFFRACTION98
1.1246-1.14620.09552490.07474727X-RAY DIFFRACTION97
1.1462-1.16960.08612420.07744602X-RAY DIFFRACTION95
1.1696-1.1950.09062530.07594789X-RAY DIFFRACTION98
1.195-1.22280.08532520.07634796X-RAY DIFFRACTION99
1.2228-1.25340.09012530.07734801X-RAY DIFFRACTION99
1.2534-1.28730.09772500.08074753X-RAY DIFFRACTION98
1.2873-1.32520.08452510.07854771X-RAY DIFFRACTION98
1.3252-1.36790.09752500.08194749X-RAY DIFFRACTION97
1.3679-1.41680.08782430.08674620X-RAY DIFFRACTION95
1.4168-1.47360.10522510.08664777X-RAY DIFFRACTION98
1.4736-1.54060.09152520.0874776X-RAY DIFFRACTION98
1.5406-1.62190.09952500.08874763X-RAY DIFFRACTION98
1.6219-1.72350.10162500.09444744X-RAY DIFFRACTION97
1.7235-1.85660.1062490.10064722X-RAY DIFFRACTION97
1.8566-2.04340.12242460.10614678X-RAY DIFFRACTION96
2.0434-2.3390.1212540.11124829X-RAY DIFFRACTION98
2.339-2.94680.15982530.12454812X-RAY DIFFRACTION98
2.9468-41.08060.15132590.13324904X-RAY DIFFRACTION97

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