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- PDB-9flf: Three-Dimensional Structure of Human Carbonic Anhydrase IX in Com... -

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Basic information

Entry
Database: PDB / ID: 9flf
TitleThree-Dimensional Structure of Human Carbonic Anhydrase IX in Complex with a Covalent Inhibitor
ComponentsCarbonic anhydrase
KeywordsLYASE / CA IX / CA 9 / carbonic anhydrase IX / carbonic anhydrase 9 / covalent inhibitor
Function / homology
Function and homology information


one-carbon metabolic process / secretion / molecular function activator activity / morphogenesis of an epithelium / carbonic anhydrase / carbonate dehydratase activity / zinc ion binding / 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
: / Carbonic anhydrase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsLeitans, J. / Tars, K.
Funding supportEuropean Union, 1items
OrganizationGrant numberCountry
European Union (EU)5.2.1.1.i.0/2/24/I/CFLA/001European Union
Citation
Journal: 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.
#1: Journal: 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
DepositionJun 5, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 18, 2024Provider: repository / Type: Initial release
Revision 1.1Jan 22, 2025Group: Database references / Category: citation / citation_author

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)114,55012
Polymers112,3584
Non-polymers2,1928
Water7,548419
1
A: Carbonic anhydrase
B: Carbonic anhydrase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,2756
Polymers56,1792
Non-polymers1,0964
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1690 Å2
ΔGint-10 kcal/mol
Surface area20020 Å2
2
C: Carbonic anhydrase
hetero molecules

D: Carbonic anhydrase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,2756
Polymers56,1792
Non-polymers1,0964
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555-y+2/3,x-y+1/3,z+1/31
Buried area1660 Å2
ΔGint-10 kcal/mol
Surface area20000 Å2
Unit cell
Length a, b, c (Å)152.110, 152.110, 172.510
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3
Components on special symmetry positions
IDModelComponents
11A-484-

HOH

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Components

#1: Protein
Carbonic anhydrase


Mass: 28089.598 Da / Num. of mol.: 4 / Mutation: C41S, N213Q
Source method: isolated from a genetically manipulated source
Details: all 4 chains are identical, two dimers. / Source: (gene. exp.) Homo sapiens (human) / Gene: CA9 / Cell line (production host): Pichia pastoris / Production host: Komagataella pastoris (fungus) / References: UniProt: A0A2R9BYT1, 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-A1IDV / 3-[[(1~{R},4~{Z})-cyclododec-4-en-1-yl]amino]-4-ethylsulfonyl-2,5,6-tris(fluoranyl)benzenesulfonamide


Mass: 482.580 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C20H29F3N2O4S2 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 419 / 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: 3.65 Å3/Da / Density % sol: 66.31 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: CRYSTALLIZATION CONDITIONS: 1.0 M DI-AMMONIUM HYDROGEN PHOSPHATE, 0.1 M SODIUM ACETATE PH 4.5, PROTEIN 10 MG/ML, 2-5 MM INHIBITOR (STOCK SOLUTION WAS 100 MM INHIBITOR DISSOLVED IN 100% ...Details: CRYSTALLIZATION CONDITIONS: 1.0 M DI-AMMONIUM HYDROGEN PHOSPHATE, 0.1 M SODIUM ACETATE PH 4.5, PROTEIN 10 MG/ML, 2-5 MM INHIBITOR (STOCK SOLUTION WAS 100 MM INHIBITOR DISSOLVED IN 100% DIMETHYL SULFOXIDE), VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 294K

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97626 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: May 19, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97626 Å / Relative weight: 1
ReflectionResolution: 2.2→52.35 Å / Num. obs: 75528 / % possible obs: 100 % / Redundancy: 10.7 % / Biso Wilson estimate: 49.468 Å2 / Rmerge(I) obs: 0.072 / Net I/σ(I): 17.2
Reflection shellResolution: 2.2→2.25 Å / Redundancy: 11 % / Rmerge(I) obs: 1.159 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 4445 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
Aimlessdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→52.35 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.958 / SU B: 4.716 / SU ML: 0.116 / Cross valid method: THROUGHOUT / ESU R: 0.168 / ESU R Free: 0.151 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20215 3874 5.1 %RANDOM
Rwork0.16775 ---
obs0.16953 71653 99.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 52.491 Å2
Baniso -1Baniso -2Baniso -3
1-0.85 Å20.42 Å2-0 Å2
2--0.85 Å20 Å2
3----2.75 Å2
Refinement stepCycle: 1 / Resolution: 2.2→52.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7516 0 0 419 7935
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0127732
X-RAY DIFFRACTIONr_bond_other_d0.0010.0167245
X-RAY DIFFRACTIONr_angle_refined_deg1.7741.86310558
X-RAY DIFFRACTIONr_angle_other_deg1.7941.74416696
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7435958
X-RAY DIFFRACTIONr_dihedral_angle_2_deg7.759565
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.914101151
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0840.21149
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.029250
X-RAY DIFFRACTIONr_gen_planes_other0.0030.021774
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_it4.7235.2573841
X-RAY DIFFRACTIONr_mcbond_other4.7215.2573841
X-RAY DIFFRACTIONr_mcangle_it6.2579.4294796
X-RAY DIFFRACTIONr_mcangle_other6.2569.4294797
X-RAY DIFFRACTIONr_scbond_it5.8555.8263891
X-RAY DIFFRACTIONr_scbond_other5.8545.8273892
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other8.31110.4615763
X-RAY DIFFRACTIONr_long_range_B_refined10.20651.748040
X-RAY DIFFRACTIONr_long_range_B_other10.20950.967971
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.312 250 -
Rwork0.257 5317 -
obs--100 %

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