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- PDB-6rnp: Human Carbonic Anhydrase II in complex with fluorinated benzenesu... -

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Basic information

Entry
Database: PDB / ID: 6rnp
TitleHuman Carbonic Anhydrase II in complex with fluorinated benzenesulfonamide
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 / cyanamide hydratase activity / regulation of chloride transport / arylesterase activity / Reversible hydration of carbon dioxide / positive regulation of synaptic transmission, GABAergic ...positive regulation of cellular pH reduction / positive regulation of dipeptide transmembrane transport / regulation of monoatomic anion transport / secretion / cyanamide hydratase / cyanamide hydratase activity / regulation of chloride transport / arylesterase activity / Reversible hydration of carbon dioxide / positive regulation of synaptic transmission, GABAergic / angiotensin-activated signaling pathway / morphogenesis of an epithelium / 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 / 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
(4-CARBOXYPHENYL)(CHLORO)MERCURY / beta-D-glucopyranose / alpha-D-glucopyranose / : / 2,5-bis(fluoranyl)benzenesulfonamide / Carbonic anhydrase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.07 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
DepositionMay 9, 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)31,3579
Polymers29,8071
Non-polymers1,5508
Water4,900272
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1190 Å2
ΔGint-23 kcal/mol
Surface area11410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.325, 41.454, 72.291
Angle α, β, γ (deg.)90.00, 104.53, 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

#6: 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
#7: 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, 277 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-KBB / 2,5-bis(fluoranyl)benzenesulfonamide


Mass: 193.171 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H5F2NO2S / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-BE7 / (4-CARBOXYPHENYL)(CHLORO)MERCURY / P-CHLOROMERCURIBENZOIC ACID


Mass: 357.156 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H5ClHgO2 / Comment: protease inhibitor*YM
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 272 / 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: Ammonium sulfate 2.7 M, TRIS 0.1 M, 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 30, 2017 / Details: Sagitally bended Si111-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: 1.07→41.454 Å / Num. obs: 104839 / % possible obs: 97.9 % / Redundancy: 3.67 % / Biso Wilson estimate: 8.3 Å2 / CC1/2: 0.998 / Rsym value: 0.06 / Net I/σ(I): 10.92
Reflection shellResolution: 1.07→1.13 Å / Redundancy: 3.55 % / Mean I/σ(I) obs: 2.07 / Num. unique obs: 16391 / CC1/2: 0.831 / Rsym value: 0.477 / % possible all: 95.2

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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: 1.07→40.971 Å / SU ML: 0.09 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 11.69
RfactorNum. reflection% reflectionSelection details
Rfree0.1361 5242 5 %Random selection of 5 %
Rwork0.1193 ---
obs0.1201 104826 97.96 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.07→40.971 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2020 0 72 272 2364
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072481
X-RAY DIFFRACTIONf_angle_d1.0193417
X-RAY DIFFRACTIONf_dihedral_angle_d15.259936
X-RAY DIFFRACTIONf_chiral_restr0.085354
X-RAY DIFFRACTIONf_plane_restr0.008474
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.0699-1.08210.36111450.38182751X-RAY DIFFRACTION81
1.0821-1.09480.25841750.27623326X-RAY DIFFRACTION99
1.0948-1.10820.23811750.21983326X-RAY DIFFRACTION99
1.1082-1.12220.1941770.18323377X-RAY DIFFRACTION99
1.1222-1.1370.18431720.16133251X-RAY DIFFRACTION98
1.137-1.15260.17531740.15753311X-RAY DIFFRACTION98
1.1526-1.1690.17531720.16073271X-RAY DIFFRACTION97
1.169-1.18650.16861680.14673181X-RAY DIFFRACTION94
1.1865-1.2050.13831760.11873343X-RAY DIFFRACTION99
1.205-1.22480.1351760.10653361X-RAY DIFFRACTION100
1.2248-1.24590.12411780.09943372X-RAY DIFFRACTION100
1.2459-1.26850.12031760.09833340X-RAY DIFFRACTION100
1.2685-1.29290.12221790.09363414X-RAY DIFFRACTION100
1.2929-1.31930.12331760.09083334X-RAY DIFFRACTION100
1.3193-1.3480.12931780.09293385X-RAY DIFFRACTION99
1.348-1.37940.12061750.09293324X-RAY DIFFRACTION99
1.3794-1.41390.12641720.0933263X-RAY DIFFRACTION96
1.4139-1.45210.12951670.09363188X-RAY DIFFRACTION95
1.4521-1.49490.11081780.09263373X-RAY DIFFRACTION100
1.4949-1.54310.12071790.0933410X-RAY DIFFRACTION100
1.5431-1.59830.10971780.09193372X-RAY DIFFRACTION100
1.5983-1.66220.12511780.09473376X-RAY DIFFRACTION100
1.6622-1.73790.11261760.09793347X-RAY DIFFRACTION99
1.7379-1.82950.10371760.10243351X-RAY DIFFRACTION99
1.8295-1.94420.12951740.10443308X-RAY DIFFRACTION97
1.9442-2.09430.12781740.11043309X-RAY DIFFRACTION98
2.0943-2.3050.12241810.11363422X-RAY DIFFRACTION100
2.305-2.63850.11821780.12393387X-RAY DIFFRACTION99
2.6385-3.3240.15061770.13983376X-RAY DIFFRACTION98
3.324-41.00120.15211820.13113435X-RAY DIFFRACTION97

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