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- PDB-3mhm: Crystal structure of human carbonic anhydrase isozyme II with 4-{... -

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Basic information

Entry
Database: PDB / ID: 3mhm
TitleCrystal structure of human carbonic anhydrase isozyme II with 4-{[N-(6-benzylamino-5-nitropyrimidin-4-yl)amino]methyl}benzenesulfonamide
ComponentsCarbonic anhydrase 2
KeywordsLYASE/LYASE INHIBITOR / drug design / carbonic anhydrase / sulfonamide / 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 / angiotensin-activated signaling pathway ...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 / angiotensin-activated signaling pathway / positive regulation of synaptic transmission, GABAergic / regulation of intracellular pH / morphogenesis of an epithelium / 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-J75 / Carbonic anhydrase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.5 Å
AuthorsGrazulis, S. / Manakova, E. / Golovenko, D.
CitationJournal: Bioorg.Med.Chem. / Year: 2010
Title: 4-[N-(Substituted 4-pyrimidinyl)amino]benzenesulfonamides as inhibitors of carbonic anhydrase isozymes I, II, VII, and XIII
Authors: Sudzius, J. / Baranauskiene, L. / Golovenko, D. / Matuliene, J. / Michailoviene, V. / Torresan, J. / Jachno, J. / Sukackaite, R. / Manakova, E. / Grazulis, S. / Tumkevicius, S. / Matulis, D.
History
DepositionApr 8, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 20, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Nov 1, 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 / diffrn_source / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _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)29,8474
Polymers29,2891
Non-polymers5583
Water5,224290
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)42.250, 41.171, 72.243
Angle α, β, γ (deg.)90.00, 104.10, 90.00
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) / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / 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-DMS / DIMETHYL SULFOXIDE / Dimethyl sulfoxide


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#4: Chemical ChemComp-J75 / 4-({[6-(benzylamino)-5-nitropyrimidin-4-yl]amino}methyl)benzenesulfonamide / 4-{[N-(6-benzylamino-5-nitropyrimidin-4-yl)amino]methyl}benzenesulfonamide


Mass: 414.438 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H18N6O4S
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 290 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsMETAL ION NATURALLY OCCURS IN CARBONIC ANHYDRASES.
Sequence details126 IS SKIPPED IN THE NUMBERING.

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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: 2.08 Å3/Da / Density % sol: 40.88 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 8
Details: 0.1M Na-bicine pH 9, 0.2M ammonium sulfate, 2.4M Na-malonate pH 7, VAPOR DIFFUSION, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X13 / Wavelength: 0.81 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Dec 18, 2009 / Details: Bent, vertically focussing mirror
RadiationMonochromator: Si (111), horizontally focussing / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.81 Å / Relative weight: 1
ReflectionResolution: 1.5→70.068 Å / Num. all: 38763 / Num. obs: 37716 / % possible obs: 97.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.1 % / Biso Wilson estimate: 14.2 Å2 / Rmerge(I) obs: 0.033 / Rsym value: 0.033 / Net I/σ(I): 25.4
Reflection shellResolution: 1.5→1.58 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.157 / Mean I/σ(I) obs: 5.8 / Num. measured all: 20829 / Num. unique all: 5409 / Rsym value: 0.157 / % possible all: 96.1

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
REFMACrefinement
MOSFLMdata reduction
SCALA3.2.25data scaling
PDB_EXTRACT3.006data extraction
MAR345v. 0.9.7 on RedHat Linux 8data collection
Omodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3HLJ

3hlj


Resolution: 1.5→39.86 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.951 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 2.359 / SU ML: 0.042 / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.097 / ESU R Free: 0.079 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18657 3760 10 %RANDOM
Rwork0.13179 33938 --
obs0.13727 37698 96.99 %-
all-38868 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 45.29 Å2 / Biso mean: 15.4 Å2 / Biso min: 4.34 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20.04 Å2
2--0.19 Å20 Å2
3----0.18 Å2
Refinement stepCycle: LAST / Resolution: 1.5→39.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2049 0 34 290 2373
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0280.0222282
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.1581.9653113
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1395282
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.96124.712104
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.83515380
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.372158
X-RAY DIFFRACTIONr_chiral_restr0.1630.2318
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.021795
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2320.21073
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3110.21500
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1470.2215
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.0790.23
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2470.285
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2590.246
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.5681.51418
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.48322228
X-RAY DIFFRACTIONr_scbond_it4.60731025
X-RAY DIFFRACTIONr_scangle_it6.0724.5885
X-RAY DIFFRACTIONr_rigid_bond_restr2.85732443
X-RAY DIFFRACTIONr_sphericity_free12.9943292
X-RAY DIFFRACTIONr_sphericity_bonded8.28132206
LS refinement shellResolution: 1.5→1.539 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.254 272 -
Rwork0.144 2474 -
all-2746 -
obs--95.75 %

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