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- PDB-6hr3: Human Carbonic Anhydrase II in complex with 4-Propylbenzenesulfonamide -

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Basic information

Entry
Database: PDB / ID: 6hr3
TitleHuman Carbonic Anhydrase II in complex with 4-Propylbenzenesulfonamide
ComponentsCarbonic anhydrase 2
KeywordsLYASE / Inhibitor / 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-propylbenzenesulfonamide / beta-D-glucopyranose / : / MERCURIBENZOIC ACID / Carbonic anhydrase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.02 Å
AuthorsGloeckner, S. / Heine, A. / Klebe, G.
CitationJournal: Acs Chem.Biol. / Year: 2020
Title: Conformational Changes in Alkyl Chains Determine the Thermodynamic and Kinetic Binding Profiles of Carbonic Anhydrase Inhibitors.
Authors: Glockner, S. / Ngo, K. / Sager, C.P. / Hufner-Wulsdorf, T. / Heine, A. / Klebe, G.
History
DepositionSep 26, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 9, 2019Provider: repository / Type: Initial release
Revision 1.1Apr 8, 2020Group: Data collection / Database references / Category: chem_comp / citation / citation_author
Item: _chem_comp.type / _citation.country ..._chem_comp.type / _citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _chem_comp.name / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Jan 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)30,7746
Polymers29,8071
Non-polymers9675
Water4,378243
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area610 Å2
ΔGint-32 kcal/mol
Surface area11470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.270, 41.519, 72.293
Angle α, β, γ (deg.)90.00, 104.59, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein / Sugars , 2 types, 2 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
#3: Sugar ChemComp-BGC / beta-D-glucopyranose / beta-D-glucose / D-glucose / glucose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 1
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

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Non-polymers , 5 types, 247 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-MBO / MERCURIBENZOIC ACID


Mass: 321.703 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H5HgO2
#5: Chemical ChemComp-HG / MERCURY (II) ION


Mass: 200.590 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Hg
#6: Chemical ChemComp-4JE / 4-propylbenzenesulfonamide


Mass: 199.270 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H13NO2S
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 243 / 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: 2.06 Å3/Da / Density % sol: 40.37 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.8
Details: Ammoniumsulfate 2.70 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: Aug 12, 2017 / Details: Sagitally bended Si111-crystal
RadiationMonochromator: Si(111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.02→41.519 Å / Num. obs: 121413 / % possible obs: 98.2 % / Observed criterion σ(I): 2 / Redundancy: 3.63 % / Biso Wilson estimate: 9.749 Å2 / CC1/2: 0.999 / Rsym value: 0.049 / Net I/σ(I): 11.6
Reflection shellResolution: 1.02→1.08 Å / Redundancy: 3.48 % / Mean I/σ(I) obs: 1.95 / Num. unique obs: 19412 / CC1/2: 0.784 / Rsym value: 0.462 / % possible all: 97.5

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3KS3

3ks3


Resolution: 1.02→34.981 Å / SU ML: 0.08 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 12.03
RfactorNum. reflection% reflectionSelection details
Rfree0.1452 6071 5 %Random selection of 5 %
Rwork0.1286 ---
obs0.1295 121409 98.25 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.02→34.981 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2010 0 37 243 2290
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082401
X-RAY DIFFRACTIONf_angle_d1.063302
X-RAY DIFFRACTIONf_dihedral_angle_d15.315894
X-RAY DIFFRACTIONf_chiral_restr0.088341
X-RAY DIFFRACTIONf_plane_restr0.008454
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.0195-1.03110.24631930.2593664X-RAY DIFFRACTION94
1.0311-1.04320.27241970.24283745X-RAY DIFFRACTION96
1.0432-1.0560.22112030.2093854X-RAY DIFFRACTION99
1.056-1.06930.21852030.18283870X-RAY DIFFRACTION99
1.0693-1.08340.17832030.1633855X-RAY DIFFRACTION99
1.0834-1.09820.16512030.14483855X-RAY DIFFRACTION99
1.0982-1.11390.1582030.13983851X-RAY DIFFRACTION99
1.1139-1.13060.16112010.12983816X-RAY DIFFRACTION99
1.1306-1.14820.14482010.12523828X-RAY DIFFRACTION98
1.1482-1.1670.14262000.12593797X-RAY DIFFRACTION97
1.167-1.18720.12582010.11973811X-RAY DIFFRACTION98
1.1872-1.20880.1422060.11343921X-RAY DIFFRACTION100
1.2088-1.2320.13932020.11223840X-RAY DIFFRACTION99
1.232-1.25720.13532030.11553845X-RAY DIFFRACTION99
1.2572-1.28450.13272040.1093883X-RAY DIFFRACTION99
1.2845-1.31440.12232020.10763842X-RAY DIFFRACTION99
1.3144-1.34720.12922030.10753850X-RAY DIFFRACTION98
1.3472-1.38370.1252020.10793833X-RAY DIFFRACTION98
1.3837-1.42440.12591980.10523763X-RAY DIFFRACTION97
1.4244-1.47040.12282040.10483881X-RAY DIFFRACTION100
1.4704-1.52290.12432060.10443911X-RAY DIFFRACTION99
1.5229-1.58390.13312040.10553878X-RAY DIFFRACTION99
1.5839-1.6560.12532040.1093880X-RAY DIFFRACTION99
1.656-1.74330.12712030.11343863X-RAY DIFFRACTION98
1.7433-1.85250.13042030.11743846X-RAY DIFFRACTION98
1.8525-1.99550.12931970.12443745X-RAY DIFFRACTION96
1.9955-2.19630.1262060.12473908X-RAY DIFFRACTION99
2.1963-2.5140.13552020.13113846X-RAY DIFFRACTION98
2.514-3.16710.18692050.14653892X-RAY DIFFRACTION98
3.1671-35.00160.15182090.13793965X-RAY DIFFRACTION98

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