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- PDB-3fw3: Crystal Structure of soluble domain of CA4 in complex with Dorzolamide -

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Basic information

Entry
Database: PDB / ID: 3fw3
TitleCrystal Structure of soluble domain of CA4 in complex with Dorzolamide
ComponentsCarbonic anhydrase 4
KeywordsLYASE / STRUCTURE-BASED DRUG DESIGN. SMALL MOLECULE COMPLEX. CO-CRYSTAL / Cell membrane / Disease mutation / Glycoprotein / GPI-anchor / Lipoprotein / Membrane / Metal-binding / Polymorphism / Retinitis pigmentosa / Sensory transduction / Vision / Zinc
Function / homology
Function and homology information


bicarbonate transport / transport vesicle membrane / endoplasmic reticulum-Golgi intermediate compartment / rough endoplasmic reticulum / secretory granule membrane / Reversible hydration of carbon dioxide / carbonic anhydrase / carbonate dehydratase activity / brush border membrane / trans-Golgi network ...bicarbonate transport / transport vesicle membrane / endoplasmic reticulum-Golgi intermediate compartment / rough endoplasmic reticulum / secretory granule membrane / Reversible hydration of carbon dioxide / carbonic anhydrase / carbonate dehydratase activity / brush border membrane / trans-Golgi network / Erythrocytes take up oxygen and release carbon dioxide / Erythrocytes take up carbon dioxide and release oxygen / one-carbon metabolic process / apical plasma membrane / external side of plasma membrane / perinuclear region of cytoplasm / Golgi apparatus / cell surface / extracellular exosome / zinc ion binding / membrane / plasma membrane
Similarity search - Function
Carbonic anhydrase, CA4/CA15 / 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. ...Carbonic anhydrase, CA4/CA15 / 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-ETS / alpha-D-glucopyranose / Carbonic anhydrase 4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.72 Å
AuthorsGreasley, S.E. / Ferre, R.A.A. / Paz, R. / Wickersham, J.
CitationJournal: Bioorg.Med.Chem. / Year: 2010
Title: Thioether benzenesulfonamide inhibitors of carbonic anhydrases II and IV: structure-based drug design, synthesis, and biological evaluation.
Authors: Vernier, W. / Chong, W. / Rewolinski, D. / Greasley, S. / Pauly, T. / Shaw, M. / Dinh, D. / Ferre, R.A. / Nukui, S. / Ornelas, M. / Reyner, E.
History
DepositionJan 16, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 1, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_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_asym_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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Carbonic anhydrase 4
B: Carbonic anhydrase 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,8819
Polymers60,7292
Non-polymers1,1527
Water4,756264
1
A: Carbonic anhydrase 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,0315
Polymers30,3641
Non-polymers6664
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Carbonic anhydrase 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,8504
Polymers30,3641
Non-polymers4863
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)49.991, 70.826, 71.774
Angle α, β, γ (deg.)90.00, 91.91, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein / Sugars , 2 types, 3 molecules AB

#1: Protein Carbonic anhydrase 4 / Carbonic anhydrase IV / CA-IV / Carbonate dehydratase IV


Mass: 30364.473 Da / Num. of mol.: 2 / Fragment: Soluble Domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CA4 / Production host: Escherichia coli (E. coli) / References: UniProt: P22748, carbonic anhydrase
#4: Sugar ChemComp-GLC / alpha-D-glucopyranose / alpha-D-glucose / D-glucose / glucose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DGlcpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-glucopyranoseCOMMON NAMEGMML 1.0
a-D-GlcpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 4 types, 270 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-ETS / (4S-TRANS)-4-(ETHYLAMINO)-5,6-DIHYDRO-6-METHYL-4H-THIENO(2,3-B)THIOPYRAN-2-SULFONAMIDE-7,7-DIOXIDE / Dorzolamide


Mass: 324.440 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N2O4S3 / Comment: medication*YM
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 264 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 2.09 Å3/Da / Density % sol: 41.18 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 4.4
Details: 25% PEG 3350, 0.1M Na Acetate, 0.20M Ammonium sulfate, 3% glucose., pH 4.4, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Dec 4, 2003
RadiationMonochromator: single crystal, cylindrically bent, Si(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.72→29.6 Å / Num. obs: 52706 / % possible obs: 99 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 2 / Redundancy: 2.81 % / Biso Wilson estimate: 19.2 Å2 / Rmerge(I) obs: 0.058 / Net I/σ(I): 18.7
Reflection shellResolution: 1.72→1.78 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.38 / Mean I/σ(I) obs: 2 / Num. unique all: 5214 / % possible all: 98.3

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
REFMAC5.1.24refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1ZNC

1znc


Resolution: 1.72→29.6 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.946 / SU B: 2.207 / SU ML: 0.072 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 1 / ESU R: 0.111 / ESU R Free: 0.106 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20637 2661 5.1 %RANDOM
Rwork0.1756 ---
obs0.17716 50026 98.63 %-
all-50026 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 18.542 Å2
Baniso -1Baniso -2Baniso -3
1-0.49 Å20 Å2-0.19 Å2
2--0.07 Å20 Å2
3----0.57 Å2
Refinement stepCycle: LAST / Resolution: 1.72→29.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3962 0 61 264 4287
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0214122
X-RAY DIFFRACTIONr_bond_other_d0.0020.023626
X-RAY DIFFRACTIONr_angle_refined_deg1.5661.9655579
X-RAY DIFFRACTIONr_angle_other_deg0.83538473
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6725493
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0950.2618
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.024452
X-RAY DIFFRACTIONr_gen_planes_other0.0110.02765
X-RAY DIFFRACTIONr_nbd_refined0.2720.2649
X-RAY DIFFRACTIONr_nbd_other0.2430.24045
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0850.22263
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.150.2183
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2340.28
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2840.235
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1150.213
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9351.52510
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.67724044
X-RAY DIFFRACTIONr_scbond_it2.52631612
X-RAY DIFFRACTIONr_scangle_it4.1764.51535
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.718→1.763 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.271 197
Rwork0.232 3477

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