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- PDB-5sz2: Carbonic anhydrase II in complex with 4-(3-formylphenyl)-benzenes... -

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Basic information

Entry
Database: PDB / ID: 5sz2
TitleCarbonic anhydrase II in complex with 4-(3-formylphenyl)-benzenesulfonamide
ComponentsCarbonic anhydrase 2
KeywordsLyase/Lyase Inhibitor / sulfonamide / inhibitor / zinc-binding / Lyase-Lyase Inhibitor complex
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 / 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 / cyanamide hydratase activity / arylesterase activity / regulation of chloride transport / Reversible hydration of carbon dioxide / morphogenesis of an epithelium / angiotensin-activated signaling pathway / positive regulation of synaptic transmission, GABAergic / 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 / apical part of cell / myelin sheath / extracellular exosome / zinc ion binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Carbonic Anhydrase II / Alpha carbonic anhydrase / 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 ...Carbonic Anhydrase II / Alpha carbonic anhydrase / 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 / Roll / Alpha Beta
Similarity search - Domain/homology
4-(3-formylphenyl)-benzenesulfonamide / Carbonic anhydrase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.63 Å
AuthorsBhatt, A. / Mahon, B.P. / Cornelio, B. / McKenna, R.
CitationJournal: Chembiochem / Year: 2017
Title: Structure-Activity Relationships of Benzenesulfonamide-Based Inhibitors towards Carbonic Anhydrase Isoform Specificity.
Authors: Bhatt, A. / Mahon, B.P. / Cruzeiro, V.W. / Cornelio, B. / Laronze-Cochard, M. / Ceruso, M. / Sapi, J. / Rance, G.A. / Khlobystov, A.N. / Fontana, A. / Roitberg, A. / Supuran, C.T. / McKenna, R.
History
DepositionAug 12, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 21, 2016Provider: repository / Type: Initial release
Revision 1.1Feb 1, 2017Group: Database references
Revision 1.2Oct 4, 2023Group: 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 / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_type.id

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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)29,9259
Polymers28,9331
Non-polymers9938
Water3,351186
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)42.444, 41.327, 71.826
Angle α, β, γ (deg.)90.000, 104.230, 90.000
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: 28932.641 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CA2 / Production host: Escherichia coli (E. coli) / References: UniProt: P00918, carbonic anhydrase

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Non-polymers , 5 types, 194 molecules

#2: Chemical ChemComp-ZN / ZINC ION


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


Mass: 78.133 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-72G / 4-(3-formylphenyl)-benzenesulfonamide / 3'-formyl[1,1'-biphenyl]-4-sulfonamide


Mass: 261.296 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C13H11NO3S
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 186 / 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: 2.11 Å3/Da / Density % sol: 41.72 %
Crystal growTemperature: 296 K / Method: vapor diffusion, sitting drop / Details: 1.6M Sodium Citrate, 50mM Tris pH 7.8 / PH range: 7.2-8.2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jan 13, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.63→20 Å / Num. obs: 49805 / % possible obs: 94.5 % / Redundancy: 5.3 % / Biso Wilson estimate: 12.38 Å2 / Rmerge(I) obs: 0.063 / Net I/av σ(I): 26.199 / Net I/σ(I): 15.4
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Diffraction-ID% possible all
1.63-1.664.40.3680.906187.4
1.66-1.694.90.3460.928190.9
1.69-1.725.20.3110.951192
1.72-1.765.30.2670.958191.1
1.76-1.795.30.2190.971192.8
1.79-1.845.40.1890.978191.6
1.84-1.885.30.1530.984194
1.88-1.935.40.130.987192.5
1.93-1.995.40.110.991194.6
1.99-2.055.40.0910.993194.2
2.05-2.135.40.0810.994194.3
2.13-2.215.40.0720.995195.2
2.21-2.315.40.0660.996195.9
2.31-2.435.30.0620.996196.2
2.43-2.595.40.0640.996196.7
2.59-2.795.40.0550.996196.6
2.79-3.065.40.0520.997196.8
3.06-3.515.30.050.996198.5
3.51-4.415.30.050.995198.4
4.41-205.10.0510.996199.3

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
HKL-2000data collection
HKL-2000data scaling
PHASERphasing
PHENIX1.10pre_2097refinement
PDB_EXTRACT3.2data extraction
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3ks3

3ks3


Resolution: 1.63→19.993 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 17.63
RfactorNum. reflection% reflection
Rfree0.1797 2490 5 %
Rwork0.1503 --
obs0.1518 49805 84.46 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 76.55 Å2 / Biso mean: 17.032 Å2 / Biso min: 6.4 Å2
Refinement stepCycle: final / Resolution: 1.63→19.993 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2049 0 83 190 2322
Biso mean--25.2 25.38 -
Num. residues----257
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062175
X-RAY DIFFRACTIONf_angle_d1.0322949
X-RAY DIFFRACTIONf_chiral_restr0.056304
X-RAY DIFFRACTIONf_plane_restr0.005376
X-RAY DIFFRACTIONf_dihedral_angle_d11.0341261
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 18

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.6303-1.66170.2738860.22771590167652
1.6617-1.69560.2308900.18561795188557
1.6956-1.73240.18341030.1681892199562
1.7324-1.77270.21611020.15482066216866
1.7727-1.8170.18591130.16522247236072
1.817-1.86610.16481470.14792396254378
1.8661-1.9210.18091330.14312615274883
1.921-1.98290.19311430.14052711285488
1.9829-2.05370.18571460.13772865301191
2.0537-2.13590.17831690.14642874304394
2.1359-2.23290.19791520.15292980313295
2.2329-2.35050.22591580.1462971312996
2.3505-2.49750.17861560.15143010316696
2.4975-2.68990.18441590.15523017317697
2.6899-2.95980.17381630.15793108327198
2.9598-3.38630.18941560.15233000315698
3.3863-4.25960.14211540.13313093324799
4.2596-19.99440.16541620.1563083324599
Refinement TLS params.Method: refined / Origin x: -5.9098 Å / Origin y: -0.2834 Å / Origin z: 85.4384 Å
111213212223313233
T0.0536 Å2-0.0043 Å2-0.0005 Å2-0.0497 Å2-0.0055 Å2--0.0537 Å2
L0.3148 °2-0.1238 °2-0.0425 °2-0.1753 °2-0.0226 °2--0.2287 °2
S0.0108 Å °-0.0151 Å °0.0138 Å °-0.0085 Å °-0.0027 Å °0.0176 Å °0.004 Å °0.0132 Å °0 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA4 - 261
2X-RAY DIFFRACTION1allB262
3X-RAY DIFFRACTION1allD2 - 202
4X-RAY DIFFRACTION1allC1 - 4
5X-RAY DIFFRACTION1allC5
6X-RAY DIFFRACTION1allE400
7X-RAY DIFFRACTION1allG1
8X-RAY DIFFRACTION1allG2

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