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- PDB-8oo8: Three-Dimensional Structure of Human Carbonic Anhydrase II in Com... -

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Basic information

Entry
Database: PDB / ID: 8oo8
TitleThree-Dimensional Structure of Human Carbonic Anhydrase II in Complex with a Covalent Inhibitor
ComponentsCarbonic anhydrase 2
KeywordsLYASE / CA II / CA 2 / carbonic anhydrase II / carbonic anhydrase 2 / covalent inhibitor
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 / positive regulation of synaptic transmission, GABAergic / regulation of intracellular pH / 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, 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
Similarity search - Domain/homology
: / Carbonic anhydrase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsLeitans, J. / Tars, K.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Elife / Year: 2024
Title: Targeted anticancer pre-vinylsulfone covalent inhibitors of carbonic anhydrase IX.
Authors: Vaskevicius, A. / Baronas, D. / Leitans, J. / Kvietkauskaite, A. / Ruksenaite, A. / Manakova, E. / Toleikis, Z. / Kaupinis, A. / Kazaks, A. / Gedgaudas, M. / Mickeviciute, A. / ...Authors: Vaskevicius, A. / Baronas, D. / Leitans, J. / Kvietkauskaite, A. / Ruksenaite, A. / Manakova, E. / Toleikis, Z. / Kaupinis, A. / Kazaks, A. / Gedgaudas, M. / Mickeviciute, A. / Juozapaitiene, V. / Schioth, H.B. / Jaudzems, K. / Valius, M. / Tars, K. / Grazulis, S. / Meyer-Almes, F.J. / Matuliene, J. / Zubriene, A. / Dudutiene, V. / Matulis, D.
History
DepositionApr 4, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 10, 2024Provider: repository / Type: Initial release
Revision 1.1Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification
Revision 1.2Jan 22, 2025Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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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)29,6523
Polymers29,1581
Non-polymers4942
Water6,089338
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area11740 Å2
Unit cell
Length a, b, c (Å)42.450, 41.570, 72.790
Angle α, β, γ (deg.)90.00, 104.40, 90.00
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: 29157.863 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CA2 / Production host: Escherichia coli (E. coli) / 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-VV8 / 3-(cyclooctylamino)-4-ethylsulfonyl-2,5,6-tris(fluoranyl)benzenesulfonamide


Mass: 428.490 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H23F3N2O4S2 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 338 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.15 Å3/Da / Density % sol: 42.73 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop
Details: A 9 0.06 M Divalents 0.1 M Buffer System 3 8.5 30 % v/v Precipitant Mix 1 0.06 M Magnesium chloride hexahydrate; 0.06 M Calcium chloride dihydrate, 0.1 M Tris pH 8.5, 20% v/v PEG 500 MME; 10 ...Details: A 9 0.06 M Divalents 0.1 M Buffer System 3 8.5 30 % v/v Precipitant Mix 1 0.06 M Magnesium chloride hexahydrate; 0.06 M Calcium chloride dihydrate, 0.1 M Tris pH 8.5, 20% v/v PEG 500 MME; 10 % w/v PEG 20000. (Morpheus A-9)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.97625 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 17, 2021
RadiationMonochromator: KMC-1 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 1.4→70.5 Å / Num. obs: 47352 / % possible obs: 96.9 % / Redundancy: 5 % / Biso Wilson estimate: 8.9 Å2 / Rmerge(I) obs: 0.143 / Net I/σ(I): 6.5
Reflection shellResolution: 1.4→1.47 Å / Redundancy: 5 % / Rmerge(I) obs: 0.482 / Mean I/σ(I) obs: 3 / Num. unique obs: 6981 / % possible all: 98

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Processing

Software
NameVersionClassification
REFMAC5.8.0350refinement
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.4→70.5 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.947 / Cross valid method: THROUGHOUT / ESU R: 0.069 / ESU R Free: 0.072 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21516 2410 5.1 %RANDOM
Rwork0.18455 ---
obs0.18614 44917 96.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 11.024 Å2
Baniso -1Baniso -2Baniso -3
1--0.33 Å20 Å2-0.19 Å2
2--0.26 Å2-0 Å2
3---0.15 Å2
Refinement stepCycle: 1 / Resolution: 1.4→70.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2068 0 0 338 2406
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0122140
X-RAY DIFFRACTIONr_bond_other_d0.0020.0161911
X-RAY DIFFRACTIONr_angle_refined_deg1.6671.6582912
X-RAY DIFFRACTIONr_angle_other_deg0.9041.584475
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0735258
X-RAY DIFFRACTIONr_dihedral_angle_2_deg9.8107
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.43710346
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0810.2304
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.022390
X-RAY DIFFRACTIONr_gen_planes_other0.0180.02419
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.2721.0791029
X-RAY DIFFRACTIONr_mcbond_other1.2681.0781029
X-RAY DIFFRACTIONr_mcangle_it1.9861.6141285
X-RAY DIFFRACTIONr_mcangle_other1.9871.6171286
X-RAY DIFFRACTIONr_scbond_it1.8651.2431111
X-RAY DIFFRACTIONr_scbond_other1.8651.2441112
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.8131.791627
X-RAY DIFFRACTIONr_long_range_B_refined4.61820.8712467
X-RAY DIFFRACTIONr_long_range_B_other4.29317.4442373
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.4→1.433 Å
RfactorNum. reflection% reflection
Rfree0.339 172 -
Rwork0.322 3392 -
obs--98.43 %

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