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- PDB-6evr: Crystal structure of human carbonic anhydrase I in complex with t... -

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Basic information

Entry
Database: PDB / ID: 6evr
TitleCrystal structure of human carbonic anhydrase I in complex with the 4-(4 acetyl-3-benzylpiperazine-1 carbonyl)benzene-1-sulfonamide inhibitor
ComponentsCarbonic anhydrase 1
KeywordsLYASE / INHIBITOR / COMPLEX
Function / homology
Function and homology information


hydro-lyase activity / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / cyanamide hydratase / cyanamide hydratase activity / arylesterase activity / Reversible hydration of carbon dioxide / carbonic anhydrase / carbonate dehydratase activity / Erythrocytes take up oxygen and release carbon dioxide / Erythrocytes take up carbon dioxide and release oxygen ...hydro-lyase activity / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / cyanamide hydratase / cyanamide hydratase activity / arylesterase activity / Reversible hydration of carbon dioxide / carbonic anhydrase / carbonate dehydratase activity / Erythrocytes take up oxygen and release carbon dioxide / Erythrocytes take up carbon dioxide and release oxygen / one-carbon metabolic process / extracellular exosome / zinc ion binding / 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
ACETATE ION / Chem-BZW / Carbonic anhydrase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.5 Å
AuthorsFerraroni, M. / Supuran, C.T. / Chiapponi, D. / Chiaramonte, N.
CitationJournal: Eur J Med Chem / Year: 2018
Title: 2-Benzylpiperazine: A new scaffold for potent human carbonic anhydrase inhibitors. Synthesis, enzyme inhibition, enantioselectivity, computational and crystallographic studies and in vivo ...Title: 2-Benzylpiperazine: A new scaffold for potent human carbonic anhydrase inhibitors. Synthesis, enzyme inhibition, enantioselectivity, computational and crystallographic studies and in vivo activity for a new class of intraocular pressure lowering agents.
Authors: Chiaramonte, N. / Bua, S. / Ferraroni, M. / Nocentini, A. / Bonardi, A. / Bartolucci, G. / Durante, M. / Lucarini, L. / Chiapponi, D. / Dei, S. / Manetti, D. / Teodori, E. / Gratteri, P. / ...Authors: Chiaramonte, N. / Bua, S. / Ferraroni, M. / Nocentini, A. / Bonardi, A. / Bartolucci, G. / Durante, M. / Lucarini, L. / Chiapponi, D. / Dei, S. / Manetti, D. / Teodori, E. / Gratteri, P. / Masini, E. / Supuran, C.T. / Romanelli, M.N.
History
DepositionNov 2, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 6, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 10, 2018Group: Data collection / Database references / Structure summary
Category: citation / citation_author / entity
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _entity.formula_weight
Revision 1.2Jan 17, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / entity / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.formula_weight / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Carbonic anhydrase 1
B: Carbonic anhydrase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,9899
Polymers57,8122
Non-polymers1,1777
Water8,161453
1
A: Carbonic anhydrase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,5245
Polymers28,9061
Non-polymers6184
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Carbonic anhydrase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,4654
Polymers28,9061
Non-polymers5593
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)62.119, 71.064, 122.122
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Carbonic anhydrase 1 / / Carbonate dehydratase I / Carbonic anhydrase B / CAB / Carbonic anhydrase I / CA-I


Mass: 28906.186 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P00915, carbonic anhydrase

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Non-polymers , 5 types, 460 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-BZW / 4-[(3~{S})-4-ethanoyl-3-(phenylmethyl)piperazin-1-yl]carbonylbenzenesulfonamide


Mass: 401.479 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H23N3O4S / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 453 / 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: 2.33 Å3/Da / Density % sol: 47.24 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 9 / Details: 28% PEG4000, 0.2 M Sodium acetate, Tris 100 mM

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.966 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Jul 15, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.966 Å / Relative weight: 1
ReflectionResolution: 1.5→19.88 Å / Num. obs: 87056 / % possible obs: 99.4 % / Observed criterion σ(I): -3 / Redundancy: 4.414 % / Biso Wilson estimate: 28.397 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.049 / Rrim(I) all: 0.055 / Χ2: 1.124 / Net I/σ(I): 13.93 / Num. measured all: 384284
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.5-1.594.4230.6542.04137000.8130.74698
1.59-1.74.2380.3923.25130330.9190.4599.4
1.7-1.834.5660.2215.77122800.9770.25199.9
1.83-2.014.6070.11910.23113270.9930.135100
2.01-2.244.4150.07515.3102480.9960.08499.8
2.24-2.594.2950.0521.8790400.9980.05699.2
2.59-3.164.5690.03730.0377610.9990.04299.9
3.16-4.454.1380.03136.5861070.9990.03599.6
4.45-19.884.3260.03140.5935590.9990.03598.1

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Processing

Software
NameVersionClassification
XSCALEdata scaling
REFMACrefinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 1JV0

1jv0


Resolution: 1.5→19.88 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.962 / SU B: 2.343 / SU ML: 0.078 / SU R Cruickshank DPI: 0.0751 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.075 / ESU R Free: 0.08 / Details: U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2227 4378 5 %RANDOM
Rwork0.1843 ---
obs0.1862 82483 99.61 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 89.91 Å2 / Biso mean: 27.172 Å2 / Biso min: 12.77 Å2
Baniso -1Baniso -2Baniso -3
1--0 Å2-0 Å2-0 Å2
2--0 Å2-0 Å2
3---0 Å2
Refinement stepCycle: final / Resolution: 1.5→19.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4009 0 74 453 4536
Biso mean--29.35 38.66 -
Num. residues----514
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.0194235
X-RAY DIFFRACTIONr_angle_refined_deg2.1511.9255775
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9565528
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.00824.817191
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.53315659
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.8081514
X-RAY DIFFRACTIONr_chiral_restr0.1690.2616
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.0213306
LS refinement shellResolution: 1.5→1.539 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.395 294 -
Rwork0.397 6034 -
all-6328 -
obs--99.64 %

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