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- PDB-9fpv: Crystal structure of carbonic anhydrase XIII with methyl 4-benzyl... -

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Basic information

Entry
Database: PDB / ID: 9fpv
TitleCrystal structure of carbonic anhydrase XIII with methyl 4-benzylsulfanyl-3-sulfamoyl-benzoate
ComponentsCarbonic anhydrase 13
KeywordsLYASE / DRUG DESIGN / CARBONIC ANHYDRASE / BENZENESULFONAMIDE / LYASE-LYASE INHIBITOR COMPLEX
Function / homology
Function and homology information


Reversible hydration of carbon dioxide / carbonic anhydrase / carbonate dehydratase activity / myelin sheath / intracellular membrane-bounded organelle / zinc ion binding / 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 13
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsSmirnov, A. / Manakova, E.N. / Grazulis, S. / Paketuryte, V.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: J.Med.Chem. / Year: 2025
Title: Affinity and Selectivity of Protein-Ligand Recognition: A Minor Chemical Modification Changes Carbonic Anhydrase Binding Profile.
Authors: Zaksauskas, A. / Paketuryte-Latve, V. / Jankunaite, A. / Capkauskaite, E. / Becart, Y. / Smirnov, A. / Pospisilova, K. / Leitans, J. / Brynda, J. / Kazaks, A. / Baranauskiene, L. / Manakova, ...Authors: Zaksauskas, A. / Paketuryte-Latve, V. / Jankunaite, A. / Capkauskaite, E. / Becart, Y. / Smirnov, A. / Pospisilova, K. / Leitans, J. / Brynda, J. / Kazaks, A. / Baranauskiene, L. / Manakova, E. / Grazulis, S. / Kairys, V. / Tars, K. / Rezacova, P. / Matulis, D.
History
DepositionJun 13, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 25, 2025Provider: repository / Type: Initial release
Revision 1.1Oct 8, 2025Group: Database references / Category: citation / citation_author
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 / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: Carbonic anhydrase 13
A: Carbonic anhydrase 13
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,0326
Polymers59,2272
Non-polymers8064
Water7,548419
1
B: Carbonic anhydrase 13
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,0163
Polymers29,6131
Non-polymers4032
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Carbonic anhydrase 13
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,0163
Polymers29,6131
Non-polymers4032
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)55.054, 57.958, 160.174
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Carbonic anhydrase 13 / Carbonate dehydratase XIII / Carbonic anhydrase XIII / CA-XIII


Mass: 29613.318 Da / Num. of mol.: 2 / Fragment: human carbonic anhydrase XIII
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CA13 / Plasmid: pET15b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q8N1Q1, carbonic anhydrase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-A1IEL / methyl 4-(phenylmethylsulfanyl)-3-sulfamoyl-benzoate


Mass: 337.414 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H15NO4S2 / 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 modificationN

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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: 2.13 Å3/Da / Density % sol: 41.8 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.1M sodium citrate pH5.5, 0.1M sodium acetate pH4.5 and 26% of PEG4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.9762 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 20, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 1.7→160.174 Å / Num. all: 57402 / Num. obs: 57402 / % possible obs: 100 % / Redundancy: 13.2 % / Rpim(I) all: 0.026 / Rrim(I) all: 0.095 / Rsym value: 0.088 / Net I/av σ(I): 5 / Net I/σ(I): 16.8 / Num. measured all: 755947
Reflection shell

Diffraction-ID: 1 / % possible all: 100

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique obsRpim(I) allRrim(I) allRsym valueNet I/σ(I) obs
1.7-1.7913.10.3232.110797882460.0950.3470.3237.4
1.79-1.912.70.22139951278440.0670.2380.2219.4
1.9-2.0313.70.1633.910065773560.0470.1760.16312.5
2.03-2.1913.50.13159275668690.0380.1410.13115.2
2.19-2.412.60.1135.68019663590.0350.1230.11316.9
2.4-2.6913.90.1016.38016557540.0290.1080.10120
2.69-3.113.50.0976917651350.0260.0970.0923.6
3.1-3.812.70.0777.85551843790.0230.0820.07728.1
3.8-5.3813.30.0659.54580234390.0190.0690.06532
5.38-160.174120.068.72418720210.0190.0650.0628.3

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Processing

Software
NameVersionClassification
SCALA3.3.22data scaling
REFMAC5.8.0232refinement
PDB_EXTRACT3.27data extraction
Cootmodel building
MOLREPphasing
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→80.09 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.953 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.104 / ESU R Free: 0.102 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1942 5801 10.1 %RANDOM
Rwork0.1576 ---
obs0.1611 51466 99.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 71.79 Å2 / Biso mean: 21.614 Å2 / Biso min: 9.26 Å2
Baniso -1Baniso -2Baniso -3
1-0.81 Å20 Å20 Å2
2--0.82 Å2-0 Å2
3----1.63 Å2
Refinement stepCycle: final / Resolution: 1.7→80.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4077 0 46 419 4542
Biso mean--31.6 32.03 -
Num. residues----515
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0124308
X-RAY DIFFRACTIONr_angle_refined_deg1.8971.6445882
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8075527
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.52322.837215
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.65215680
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.9741520
X-RAY DIFFRACTIONr_chiral_restr0.1330.2540
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.023381
LS refinement shellResolution: 1.7→1.744 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.201 418 -
Rwork0.157 3728 -
all-4146 -
obs--99.64 %

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