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- PDB-6sbh: Human Carbonic Anhydrase II in complex with 4-pentylbenzenesulfon... -

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Basic information

Entry
Database: PDB / ID: 6sbh
TitleHuman Carbonic Anhydrase II in complex with 4-pentylbenzenesulfonamide.
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 / : / 4-pentylbenzenesulfonamide / Carbonic anhydrase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 0.95 Å
AuthorsGloeckner, S. / Ngo, K. / 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
DepositionJul 20, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 8, 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

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Assembly

Deposited unit
A: Carbonic anhydrase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,1988
Polymers29,8071
Non-polymers1,3917
Water4,035224
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1170 Å2
ΔGint-28 kcal/mol
Surface area11420 Å2
Unit cell
Length a, b, c (Å)42.294, 41.530, 72.165
Angle α, β, γ (deg.)90.000, 104.523, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb

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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
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, 228 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 / Comment: protease inhibitor*YM
#5: Chemical ChemComp-L4K / 4-pentylbenzenesulfonamide


Mass: 227.323 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H17NO2S / Feature type: SUBJECT OF INVESTIGATION
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 224 / 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: 40.33 %
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 12, 2017
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: 0.95→41.53 Å / Num. obs: 142312 / % possible obs: 93.2 % / Redundancy: 3.77 % / Biso Wilson estimate: 8.12 Å2 / CC1/2: 0.996 / Rsym value: 0.071 / Net I/σ(I): 9.27
Reflection shellResolution: 0.95→1.01 Å / Redundancy: 3.6 % / Mean I/σ(I) obs: 2.09 / Num. unique obs: 21669 / CC1/2: 0.852 / Rsym value: 0.361 / % possible all: 88.1

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3KS3

3ks3


Resolution: 0.95→34.93 Å / SU ML: 0.0819 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 10.4542
RfactorNum. reflection% reflectionSelection details
Rfree0.1337 7116 5 %Random selection of 5 %
Rwork0.1201 ---
obs0.1208 135196 93.25 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 11.6 Å2
Refinement stepCycle: LAST / Resolution: 0.95→34.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2010 0 63 224 2297
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00782622
X-RAY DIFFRACTIONf_angle_d1.05533611
X-RAY DIFFRACTIONf_chiral_restr0.0846376
X-RAY DIFFRACTIONf_plane_restr0.008490
X-RAY DIFFRACTIONf_dihedral_angle_d13.4112980
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
0.95-0.960.19942050.20153899X-RAY DIFFRACTION80.49
0.96-0.970.18982270.17534308X-RAY DIFFRACTION89.39
0.97-0.980.18982260.16554288X-RAY DIFFRACTION89.83
0.98-10.18232290.1684354X-RAY DIFFRACTION91.35
1-1.010.18542310.16754392X-RAY DIFFRACTION90.47
1.01-1.020.19252300.16834375X-RAY DIFFRACTION91.26
1.02-1.040.18352270.17374315X-RAY DIFFRACTION89.32
1.04-1.050.14382310.13164381X-RAY DIFFRACTION91.45
1.05-1.070.12722330.11374434X-RAY DIFFRACTION92.16
1.07-1.090.11462340.09974434X-RAY DIFFRACTION92.02
1.09-1.110.11572340.10144448X-RAY DIFFRACTION92.8
1.11-1.130.1132350.10074472X-RAY DIFFRACTION92.75
1.13-1.150.11672360.10144483X-RAY DIFFRACTION92.69
1.15-1.170.12172310.10214393X-RAY DIFFRACTION91.37
1.17-1.20.11192370.1014499X-RAY DIFFRACTION93.65
1.2-1.220.10882400.09864557X-RAY DIFFRACTION93.89
1.22-1.250.12652370.09584507X-RAY DIFFRACTION94.09
1.25-1.290.11082400.0934563X-RAY DIFFRACTION94.34
1.29-1.330.1022400.09334562X-RAY DIFFRACTION94.92
1.33-1.370.10222430.09644599X-RAY DIFFRACTION94.89
1.37-1.420.11812350.09784476X-RAY DIFFRACTION92.59
1.42-1.480.11232440.09844639X-RAY DIFFRACTION95.93
1.48-1.540.10832440.0994640X-RAY DIFFRACTION96.22
1.54-1.620.11232470.10194680X-RAY DIFFRACTION96.78
1.62-1.730.12942480.10674719X-RAY DIFFRACTION96.97
1.73-1.860.12392470.11094689X-RAY DIFFRACTION96.88
1.86-2.050.1262430.11534611X-RAY DIFFRACTION94.86
2.05-2.340.13032530.12074809X-RAY DIFFRACTION98.46
2.34-2.950.14162530.13984819X-RAY DIFFRACTION98.37
2.95-34.930.16332560.14054844X-RAY DIFFRACTION96.92

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