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- PDB-8co3: Three dimensional structure of human carbonic anhydrase XII in co... -

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Basic information

Entry
Database: PDB / ID: 8co3
TitleThree dimensional structure of human carbonic anhydrase XII in complex with sulfonamide
ComponentsCarbonic anhydrase 12
KeywordsLYASE / CA XII / CA 12 / carbonic anhydrase XII / carbonic anhydrase 12
Function / homology
Function and homology information


chloride ion homeostasis / estrous cycle / Reversible hydration of carbon dioxide / carbonic anhydrase / carbonate dehydratase activity / one-carbon metabolic process / basolateral plasma membrane / apical plasma membrane / zinc ion binding / membrane / plasma membrane
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
Chem-V8O / Carbonic anhydrase 12
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.68 Å
AuthorsLeitans, J. / Dvinskis, E. / Tars, K.
Funding support Latvia, 1items
OrganizationGrant numberCountry
Not funded Latvia
CitationJournal: J.Med.Chem. / Year: 2023
Title: Atropo/Tropo Flexibility: A Tool for Design and Synthesis of Self-Adaptable Inhibitors of Carbonic Anhydrases and Their Antiproliferative Effect.
Authors: Ivanova, J.N. / Nocentini, A. / Ta Rs, K. / Leita Ns, J.N. / Dvinskis, E. / Kazaks, A. / Domraceva, I. / Supuran, C.T. / Zalubovskis, R.
History
DepositionFeb 26, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 13, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Carbonic anhydrase 12
B: Carbonic anhydrase 12
C: Carbonic anhydrase 12
D: Carbonic anhydrase 12
hetero molecules


Theoretical massNumber of molelcules
Total (without water)121,21612
Polymers119,4294
Non-polymers1,7888
Water21,6541202
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5830 Å2
ΔGint-2 kcal/mol
Surface area42730 Å2
Unit cell
Length a, b, c (Å)46.780, 67.480, 81.000
Angle α, β, γ (deg.)81.47, 84.09, 86.45
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Carbonic anhydrase 12 / / Carbonate dehydratase XII / Carbonic anhydrase XII / CA-XII / Tumor antigen HOM-RCC-3.1.3


Mass: 29857.201 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: dimers / Source: (gene. exp.) Homo sapiens (human) / Gene: CA12 / Production host: Escherichia coli (E. coli) / References: UniProt: O43570, carbonic anhydrase
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-V8O / 5-(5-methyl-6-quinolin-5-yl-pyridin-3-yl)thiophene-2-sulfonamide


Mass: 381.471 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C19H15N3O2S2 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1202 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 41.63 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop
Details: 0.2M AMMONIUM ACETATE, 0.1M SODIUM CITRATE, PH 5.6, 31% PEG 4000, PROTEIN 10 MG/ML, 5-10 MM INHIBITOR (STOCK SOLUTION WAS DISSOLVED IN 100% DMSO), VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 294K

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 27, 2019
RadiationMonochromator: KMC-1 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.68→79.74 Å / Num. obs: 94857 / % possible obs: 85.5 % / Redundancy: 3.1 % / Biso Wilson estimate: 9.8 Å2 / Rmerge(I) obs: 0.164 / Net I/σ(I): 4.5
Reflection shellResolution: 1.68→1.77 Å / Redundancy: 3 % / Rmerge(I) obs: 0.561 / Mean I/σ(I) obs: 2 / Num. unique obs: 13891 / % possible all: 85.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0350refinement
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.68→79.74 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.908 / SU B: 3.703 / SU ML: 0.119 / Cross valid method: THROUGHOUT / ESU R: 0.155 / ESU R Free: 0.15 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25406 4734 5 %RANDOM
Rwork0.19939 ---
obs0.2022 90109 85.46 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 14.067 Å2
Baniso -1Baniso -2Baniso -3
1--1.39 Å2-0.26 Å2-0.05 Å2
2--0.45 Å20.02 Å2
3---0.85 Å2
Refinement stepCycle: 1 / Resolution: 1.68→79.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8330 0 108 1202 9640
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0128730
X-RAY DIFFRACTIONr_bond_other_d0.0080.0167380
X-RAY DIFFRACTIONr_angle_refined_deg1.4881.66111913
X-RAY DIFFRACTIONr_angle_other_deg0.5031.55617287
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.62751040
X-RAY DIFFRACTIONr_dihedral_angle_2_deg17.7731031
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.292101335
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0660.21242
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.029897
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021767
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_it1.1491.484160
X-RAY DIFFRACTIONr_mcbond_other1.1481.484160
X-RAY DIFFRACTIONr_mcangle_it1.892.2145194
X-RAY DIFFRACTIONr_mcangle_other1.892.2145195
X-RAY DIFFRACTIONr_scbond_it1.3841.654570
X-RAY DIFFRACTIONr_scbond_other1.3841.654571
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.2112.4156718
X-RAY DIFFRACTIONr_long_range_B_refined4.67628.88910004
X-RAY DIFFRACTIONr_long_range_B_other4.39624.7159666
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.68→1.724 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.33 352 -
Rwork0.298 6779 -
obs--86.23 %

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