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- PDB-6sb7: Human Carbonic Anhydrase II in complex with fragment. -

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Basic information

Entry
Database: PDB / ID: 6sb7
TitleHuman Carbonic Anhydrase II in complex with fragment.
ComponentsCarbonic anhydrase 2
KeywordsLYASE / Inhibitor / Complex / CO2 conversion / fragment
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
5-chloranylthiophene-2-sulfonamide / (4-CARBOXYPHENYL)(CHLORO)MERCURY / : / Carbonic anhydrase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.09 Å
AuthorsGloeckner, S. / Heine, A. / Klebe, G.
CitationJournal: Biomolecules / Year: 2020
Title: A Proof-of-Concept Fragment Screening of a Hit-Validated 96-Compounds Library against Human Carbonic Anhydrase II.
Authors: Glockner, S. / Heine, A. / Klebe, G.
History
DepositionJul 19, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 15, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_symmetry

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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)31,43111
Polymers29,8071
Non-polymers1,62510
Water2,720151
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1590 Å2
ΔGint-75 kcal/mol
Surface area11260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.497, 41.657, 72.496
Angle α, β, γ (deg.)90.000, 104.333, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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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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Non-polymers , 8 types, 161 molecules

#2: Chemical ChemComp-HG / MERCURY (II) ION


Mass: 200.590 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Hg
#3: Chemical ChemComp-ZN / ZINC ION


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


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#6: Chemical ChemComp-BE7 / (4-CARBOXYPHENYL)(CHLORO)MERCURY / P-CHLOROMERCURIBENZOIC ACID


Mass: 357.156 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H5ClHgO2 / Comment: protease inhibitor*YM
#7: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#8: Chemical ChemComp-8K2 / 5-chloranylthiophene-2-sulfonamide


Mass: 197.663 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H4ClNO2S2 / Feature type: SUBJECT OF INVESTIGATION
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 151 / 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: 2.15 Å3/Da / Density % sol: 42.89 %
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: 14.2 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS3 S 2M / Detector: PIXEL / Date: Mar 10, 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: 1.09→41.66 Å / Num. obs: 98467 / % possible obs: 97.2 % / Redundancy: 3.61 % / Biso Wilson estimate: 8.14 Å2 / CC1/2: 0.998 / Rsym value: 0.052 / Net I/σ(I): 13.47
Reflection shellResolution: 1.09→1.16 Å / Redundancy: 3.48 % / Mean I/σ(I) obs: 4.5 / Num. unique obs: 14806 / CC1/2: 0.93 / Rsym value: 0.233 / % possible all: 91.1

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3KS3

3ks3


Resolution: 1.09→35.83 Å / SU ML: 0.0778 / Cross valid method: FREE R-VALUE / σ(F): 1.41 / Phase error: 9.8529
RfactorNum. reflection% reflectionSelection details
Rfree0.1367 4924 5 %Random selection of 5 %
Rwork0.1183 ---
obs0.1192 98465 97.24 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 11.43 Å2
Refinement stepCycle: LAST / Resolution: 1.09→35.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2002 0 47 151 2200
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00942338
X-RAY DIFFRACTIONf_angle_d1.10733218
X-RAY DIFFRACTIONf_chiral_restr0.0884333
X-RAY DIFFRACTIONf_plane_restr0.0085437
X-RAY DIFFRACTIONf_dihedral_angle_d11.9426845
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.09-1.110.26491160.23892194X-RAY DIFFRACTION70.71
1.11-1.120.14481630.15413105X-RAY DIFFRACTION95.3
1.12-1.130.15541600.13033030X-RAY DIFFRACTION96.61
1.13-1.150.14091620.11653095X-RAY DIFFRACTION95.79
1.15-1.160.14491650.11273117X-RAY DIFFRACTION97.74
1.16-1.180.11151600.10533050X-RAY DIFFRACTION96.14
1.18-1.20.12751640.10283107X-RAY DIFFRACTION97.96
1.2-1.210.12591660.10243154X-RAY DIFFRACTION96.93
1.21-1.230.11331630.09973094X-RAY DIFFRACTION98.58
1.23-1.250.12791640.09813120X-RAY DIFFRACTION97.3
1.25-1.270.11961640.09793126X-RAY DIFFRACTION98.8
1.27-1.30.11691680.09743183X-RAY DIFFRACTION97.78
1.3-1.320.12251630.09783102X-RAY DIFFRACTION98.49
1.32-1.350.11681670.09373174X-RAY DIFFRACTION98.7
1.35-1.380.12221650.09593139X-RAY DIFFRACTION98.3
1.38-1.410.11111650.09583133X-RAY DIFFRACTION98.51
1.41-1.450.121670.09643177X-RAY DIFFRACTION98.82
1.45-1.490.12521670.09553163X-RAY DIFFRACTION98.58
1.49-1.530.121660.09583150X-RAY DIFFRACTION98.72
1.53-1.580.1131660.09863156X-RAY DIFFRACTION98.05
1.58-1.630.12791650.0983136X-RAY DIFFRACTION98.45
1.63-1.70.11851690.10243204X-RAY DIFFRACTION98.91
1.7-1.780.12511660.10593161X-RAY DIFFRACTION98.84
1.78-1.870.12621660.10453157X-RAY DIFFRACTION98.99
1.87-1.990.11051690.11223209X-RAY DIFFRACTION99.03
1.99-2.140.11161670.11253181X-RAY DIFFRACTION99.05
2.14-2.360.14091690.11613195X-RAY DIFFRACTION98.82
2.36-2.70.15041670.13253191X-RAY DIFFRACTION98.59
2.7-3.40.15971700.14473213X-RAY DIFFRACTION98.63
3.4-35.830.17191750.1493325X-RAY DIFFRACTION99.46

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