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- PDB-3ml2: Human carbonic anhydsase II in complex with an aryl sulfonamide i... -

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Basic information

Entry
Database: PDB / ID: 3ml2
TitleHuman carbonic anhydsase II in complex with an aryl sulfonamide inhibitor
ComponentsCarbonic anhydrase 2
Keywordslyase/lyase inhibitor / ZINC METALLOENZYME / METAL-BINDING / LYASE / SULFONAMIDE / ZINC LIGANDS / INHIBITOR / 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 / 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 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
Chem-SU0 / Carbonic anhydrase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsAvvaru, B.S. / Wagner, J. / Robbins, A.H. / Mckenna, R.
CitationJournal: Bioorg.Med.Chem. / Year: 2010
Title: Coumarinyl-substituted sulfonamides strongly inhibit several human carbonic anhydrase isoforms: solution and crystallographic investigations.
Authors: Wagner, J. / Avvaru, B.S. / Robbins, A.H. / Scozzafava, A. / Supuran, C.T. / McKenna, R.
History
DepositionApr 16, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 20, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 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 / pdbx_struct_conn_angle / struct_conn / struct_site
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_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_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)29,8354
Polymers29,2891
Non-polymers5463
Water3,333185
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)42.140, 41.200, 71.580
Angle α, β, γ (deg.)90.000, 104.130, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Carbonic anhydrase 2 / Carbonic anhydrase II / CA-II / Carbonate dehydratase II / Carbonic anhydrase C / CAC


Mass: 29289.062 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CA2, HCA2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)PLYSS / References: UniProt: P00918, carbonic anhydrase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-SU0 / 2-(7-methoxy-2-oxo-2H-chromen-4-yl)-N-(4-sulfamoylphenyl)acetamide


Mass: 388.394 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H16N2O6S
#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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 185 / 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: 40.21 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.8
Details: 1.3M sodium citrate, 100mm tris-hcl, pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Mar 2, 2010 / Details: mirrors
RadiationMonochromator: Rigaku Varimax / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.8→26.5 Å / Num. all: 19895 / Num. obs: 19803 / % possible obs: 88.6 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 2 / Redundancy: 3.3 % / Biso Wilson estimate: 34.6 Å2 / Rsym value: 0.065 / Net I/σ(I): 10.6
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 3.5 % / Mean I/σ(I) obs: 3.2 / Num. unique all: 1860 / Rsym value: 0.216 / % possible all: 89

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Processing

Software
NameVersionClassificationNB
d*TREK9.9.8.6 W9RSSIdata scaling
PHENIX1.6.1_348refinement
PDB_EXTRACT3.1data extraction
CrystalCleardata collection
d*TREKdata reduction
PHENIX1.6.1_348phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2ILI

2ili


Resolution: 1.8→23.138 Å / Occupancy max: 1 / Occupancy min: 0.42 / SU ML: 0.23 / Isotropic thermal model: isotropic with TLS / Cross valid method: THROUGHOUT / σ(F): 1.94 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.222 997 5.04 %random
Rwork0.187 ---
all0.19 19895 --
obs0.189 19784 88.56 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 33.367 Å2 / ksol: 0.46 e/Å3
Displacement parametersBiso max: 108.68 Å2 / Biso mean: 28.099 Å2 / Biso min: 10.43 Å2
Baniso -1Baniso -2Baniso -3
1--0.444 Å2-0 Å20.431 Å2
2---6.573 Å20 Å2
3---7.016 Å2
Refinement stepCycle: LAST / Resolution: 1.8→23.138 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2049 0 34 185 2268
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0182161
X-RAY DIFFRACTIONf_angle_d1.6962937
X-RAY DIFFRACTIONf_chiral_restr0.106301
X-RAY DIFFRACTIONf_plane_restr0.01379
X-RAY DIFFRACTIONf_dihedral_angle_d14.721811
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.8-1.8950.3321490.2362647279688
1.895-2.0130.3151170.2172640275787
2.013-2.1690.251400.1992568270886
2.169-2.3870.2761340.1882555268985
2.387-2.7320.2241390.1862621276086
2.732-3.440.2121440.1592766291091
3.44-23.140.1631740.1612990316496
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.4941-0.08110.00370.19920.00680.3429-0.005-0.039-0.0073-0.04190.01540.0206-0.0076-0.0241-00.1309-0.00520.00320.12090.00140.1252-9.5931-1.404415.7511
20.0182-0.00360.00230.00490.00570.00890.03510.11250.1447-0.05150.004-0.0561-0.09320.0908-0.00120.3392-0.07940.04550.1909-0.01880.226-3.54566.933913.9907
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain A and not element HA0
2X-RAY DIFFRACTION2chain I and not element HA - I0

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