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- PDB-4mdg: Closo Carborane Carbonic Anhydrase Inhibitor -

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Basic information

Entry
Database: PDB / ID: 4mdg
TitleCloso Carborane Carbonic Anhydrase Inhibitor
ComponentsCarbonic anhydrase 2
KeywordsLYASE/LYASE INHIBITOR / carbonic anhydrase inhibitor complex / 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-25X / Carbonic anhydrase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 Å
AuthorsBrynda, J. / Mader, P. / Rezacova, P.
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2013
Title: Carborane-based carbonic anhydrase inhibitors.
Authors: Brynda, J. / Mader, P. / Sicha, V. / Fabry, M. / Poncova, K. / Bakardiev, M. / Gruner, B. / Cigler, P. / Rezacova, P.
History
DepositionAug 22, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 1, 2014Provider: repository / Type: Initial release
Revision 1.1Mar 18, 2015Group: Structure summary
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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

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Assembly

Deposited unit
A: Carbonic anhydrase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,3773
Polymers29,0711
Non-polymers3072
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)42.100, 41.570, 72.130
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 / / Carbonate dehydratase II / Carbonic anhydrase C / CAC / Carbonic anhydrase II / CA-II


Mass: 29070.785 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / 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-25X / 1-(sulfamoylamino)methyl-1,2-dicarba-closo-dodecaborane


Mass: 241.259 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H5B10N2O2S
#4: Water ChemComp-HOH / water / 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: 2.11 Å3/Da / Density % sol: 41.58 %

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.9184 Å
DetectorType: RAYONIX MX-225 / Detector: CCD
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.35→69.948 Å / Num. all: 48024 / Num. obs: 48024 / % possible obs: 90.2 % / Redundancy: 2.5 % / Rsym value: 0.094 / Net I/σ(I): 5.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.35-1.392.40.3422.2475820190.34251.5
1.39-1.422.40.3092.4573423760.30962.7
1.42-1.462.50.2862.5738929850.28680.3
1.46-1.512.60.2373887334540.23795.4
1.51-1.562.60.2023.4858433350.20295.9
1.56-1.612.60.1773.8840232610.17796.3
1.61-1.672.60.1594.2811731470.15996.5
1.67-1.742.60.1394.2780830460.13996.8
1.74-1.822.60.1164.9750029110.11697.1
1.82-1.912.60.0956.2727328310.09597.3
1.91-2.012.60.0945687026660.09497.6
2.01-2.132.60.0815.9657325620.08198.2
2.13-2.282.60.0776615724070.07798.4
2.28-2.462.60.0785.7577222490.07898
2.46-2.72.60.0775.3528120580.07798.7
2.7-3.022.50.0844.7484819070.08498.8
3.02-3.492.50.0964.2428216800.09699.4
3.49-4.272.50.0864.7356814210.08699.2
4.27-6.042.50.0786.1277211110.07899
6.04-25.3672.30.0678.114005980.06794.3

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALA3.3.16data scaling
REFMACrefinement
PDB_EXTRACT3.11data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.35→24.59 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.963 / WRfactor Rfree: 0.2033 / WRfactor Rwork: 0.1602 / Occupancy max: 1 / Occupancy min: 0.2 / FOM work R set: 0.9038 / SU B: 1.809 / SU ML: 0.037 / SU R Cruickshank DPI: 0.0622 / SU Rfree: 0.0585 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.062 / ESU R Free: 0.058 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.179 2430 5.1 %RANDOM
Rwork0.1444 ---
obs0.1462 48010 89.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 59.04 Å2 / Biso mean: 17.5702 Å2 / Biso min: 5.99 Å2
Baniso -1Baniso -2Baniso -3
1-0.2 Å20 Å20.23 Å2
2--0.27 Å20 Å2
3----0.36 Å2
Refinement stepCycle: LAST / Resolution: 1.35→24.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2035 0 19 258 2312
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.022220
X-RAY DIFFRACTIONr_bond_other_d0.0020.021499
X-RAY DIFFRACTIONr_angle_refined_deg1.5011.9923122
X-RAY DIFFRACTIONr_angle_other_deg1.22933678
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4275283
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.11824.712104
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.9815360
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.094158
X-RAY DIFFRACTIONr_chiral_restr0.0970.2317
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0212476
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02444
X-RAY DIFFRACTIONr_rigid_bond_restr5.4432000
X-RAY DIFFRACTIONr_sphericity_bonded11.48951958
LS refinement shellResolution: 1.35→1.385 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.269 109 -
Rwork0.206 1853 -
all-1962 -
obs--50.63 %

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