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- PDB-3n4b: Crystal structure of human carbonic anhydrase II in complex with ... -

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Basic information

Entry
Database: PDB / ID: 3n4b
TitleCrystal structure of human carbonic anhydrase II in complex with a benzenesulfonamide inhibitor
ComponentsCarbonic anhydrase 2
KeywordsLYASE/LYASE INHIBITOR / lyase / zinc metalloenzyme / zinc ligands / benzenesulfonamide / 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 activity / cyanamide hydratase / 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 activity / cyanamide hydratase / arylesterase activity / regulation of chloride transport / Reversible hydration of carbon dioxide / morphogenesis of an epithelium / angiotensin-activated signaling pathway / regulation of intracellular pH / positive regulation of synaptic transmission, GABAergic / 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 / cytoplasm / cytosol
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-WWZ / Carbonic anhydrase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsAvvaru, B.S. / Wagner, J. / Robbins, A.H. / McKenna, R.
CitationJournal: Chem.Commun.(Camb.) / Year: 2010
Title: Selective hydrophobic pocket binding observed within the carbonic anhydrase II active site accommodate different 4-substituted-ureido-benzenesulfonamides and correlate to inhibitor potency.
Authors: Pacchiano, F. / Aggarwal, M. / Avvaru, B.S. / Robbins, A.H. / Scozzafava, A. / McKenna, R. / Supuran, C.T.
History
DepositionMay 21, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 9, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software
Revision 1.3Sep 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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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_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.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_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)29,7564
Polymers29,2891
Non-polymers4673
Water4,648258
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)42.465, 41.414, 72.037
Angle α, β, γ (deg.)90.000, 104.130, 90.000
Int Tables number4
Space group name H-MP1211
Detailsthe biological assemply is a monomer

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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 / Fragment: human carbonic anhydrase II / Mutation: wt
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: 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-WWZ / 4-{[(4-fluorophenyl)carbamoyl]amino}benzenesulfonamide


Mass: 309.316 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H12FN3O3S
#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.: 258 / 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: 2.1 Å3/Da / Density % sol: 41.35 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.8
Details: 0.05 M tris-HCl, 1.3 M sodium citrate, 5 uL + 5 uL droplet, 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: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Apr 16, 2010 / Details: mirrors
RadiationMonochromator: Rigaku varimax / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.6→19.9 Å / Num. all: 30066 / Num. obs: 30066 / % possible obs: 93.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7 % / Biso Wilson estimate: 25.1 Å2 / Rmerge(I) obs: 0.067 / Rsym value: 0.067 / Χ2: 1.056 / Net I/σ(I): 13
Reflection shellResolution: 1.6→1.66 Å / Redundancy: 7.1 % / Mean I/σ(I) obs: 3.5 / Num. unique all: 2883 / Χ2: 1.084 / % possible all: 90.1

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIXdev_403refinement
PDB_EXTRACT3.1data extraction
CrystalCleardata collection
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2ILI

2ili


Resolution: 1.6→19.853 Å / Occupancy max: 1 / Occupancy min: 0.21 / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.17 1497 4.99 %random
Rwork0.141 ---
all0.143 30066 --
obs0.143 30000 92.98 %-
Solvent computationShrinkage radii: 0.53 Å / VDW probe radii: 0.7 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 56.951 Å2 / ksol: 0.504 e/Å3
Displacement parametersBiso max: 76.4 Å2 / Biso mean: 19.149 Å2 / Biso min: 6.91 Å2
Baniso -1Baniso -2Baniso -3
1--1.097 Å20 Å20.153 Å2
2---0.329 Å20 Å2
3---1.425 Å2
Refine analyzeLuzzati coordinate error obs: 0.136 Å
Refinement stepCycle: LAST / Resolution: 1.6→19.853 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2059 0 28 258 2345
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012238
X-RAY DIFFRACTIONf_angle_d1.343055
X-RAY DIFFRACTIONf_chiral_restr0.087313
X-RAY DIFFRACTIONf_plane_restr0.007400
X-RAY DIFFRACTIONf_dihedral_angle_d13.55840
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 11

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.6-1.6520.3091360.2692424256088
1.652-1.7110.2551300.2032512264291
1.711-1.7790.1771300.1562512264291
1.779-1.860.1811380.1332537267591
1.86-1.9580.1661270.1222509263691
1.958-2.0810.1811270.1242493262089
2.081-2.2410.1741370.1322559269692
2.241-2.4660.161390.1272648278795
2.466-2.8220.1531400.132706284697
2.822-3.5530.1551460.1282745289198
3.553-19.8550.1591470.152858300599
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)
10.4131-0.13580.04740.3842-0.01280.3694-0.0078-0.01580.007-0.0190.00930.00580.01410.0088-0.00370.076-0.0040.00140.08860.00250.0771-9.4397-1.752615.7834
20.12730.1964-0.06140.4497-0.14160.0446-0.0190.00740.0163-0.0013-0.00690.0002-0.01740.01370.01180.1371-0.02670.00630.0881-0.00380.1008-3.59254.84814.8462
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain A or element ZN and not element HA0
2X-RAY DIFFRACTION2chain I and not element HA - I0

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