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- PDB-6uh0: Human Carbonic Anhydrase 2 in complex with SB4-202 -

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Basic information

Entry
Database: PDB / ID: 6uh0
TitleHuman Carbonic Anhydrase 2 in complex with SB4-202
ComponentsCarbonic anhydrase 2
KeywordsLYASE/LYASE INHIBITOR / cyclical sulfonamide / inhibitor / LYASE / LYASE-LYASE INHIBITOR complex
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
Chem-PX7 / Carbonic anhydrase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.306 Å
AuthorsMurray, A.B. / Lomelino, C.L. / McKenna, R.
CitationJournal: J.Med.Chem. / Year: 2020
Title: "A Sweet Combination": Developing Saccharin and Acesulfame K Structures for Selectively Targeting the Tumor-Associated Carbonic Anhydrases IX and XII.
Authors: Bua, S. / Lomelino, C. / Murray, A.B. / Osman, S.M. / ALOthman, Z.A. / Bozdag, M. / Abdel-Aziz, H.A. / Eldehna, W.M. / McKenna, R. / Nocentini, A. / Supuran, C.T.
History
DepositionSep 26, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 18, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 22, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation.year / _citation_author.name
Revision 1.2Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)29,2103
Polymers28,9331
Non-polymers2782
Water4,540252
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area11700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.301, 41.285, 71.913
Angle α, β, γ (deg.)90.000, 104.290, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Carbonic anhydrase 2


Mass: 28932.641 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P00918
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-PX7 / 4-methyl-1lambda~6~,2,4-benzothiadiazine-1,1,3(2H,4H)-trione


Mass: 212.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H8N2O3S / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 252 / 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: 2.1 Å3/Da / Density % sol: 41.52 %
Crystal growTemperature: 300 K / Method: vapor diffusion, hanging drop / Details: 1.6 M sodium citrate, 50 mM Tris

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.9775 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 25, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9775 Å / Relative weight: 1
ReflectionResolution: 1.306→32.04 Å / Num. obs: 55780 / % possible obs: 95.2 % / Redundancy: 6.4 % / Biso Wilson estimate: 12.48 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.041 / Rpim(I) all: 0.017 / Rrim(I) all: 0.045 / Net I/σ(I): 24.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.31-1.3340.471748718950.8180.260.5422.865.9
7.15-32.0460.02823453890.9990.0120.0360.598.8

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Processing

Software
NameVersionClassification
Aimless0.5.32data scaling
PHENIX1.11.1_2575refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3KS3

3ks3


Resolution: 1.306→29.089 Å / SU ML: 0.11 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 15.77
RfactorNum. reflection% reflection
Rfree0.1639 2750 4.93 %
Rwork0.1473 --
obs0.1481 55768 95.1 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 82.88 Å2 / Biso mean: 18.9406 Å2 / Biso min: 7.24 Å2
Refinement stepCycle: final / Resolution: 1.306→29.089 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2049 0 22 252 2323
Biso mean--20.55 26.22 -
Num. residues----257
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072146
X-RAY DIFFRACTIONf_angle_d1.0452919
X-RAY DIFFRACTIONf_chiral_restr0.082301
X-RAY DIFFRACTIONf_plane_restr0.007379
X-RAY DIFFRACTIONf_dihedral_angle_d15.321782
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.306-1.32810.23711030.2264180765
1.3281-1.35230.22021350.203201375
1.3523-1.37830.19861240.1808240086
1.3783-1.40640.19641260.1733270096
1.4064-1.4370.18841000.1677269897
1.437-1.47040.19671130.1602272597
1.4704-1.50720.19671380.152273998
1.5072-1.54790.16831480.1497267498
1.5479-1.59350.15241450.1456272498
1.5935-1.64490.17441470.1434271798
1.6449-1.70370.15211390.1441274999
1.7037-1.77190.1571550.1411273199
1.7719-1.85250.16241530.1424274799
1.8525-1.95020.14431300.1411275399
1.9502-2.07230.15681560.1398275699
2.0723-2.23230.14861540.13452771100
2.2323-2.45680.15961270.13952809100
2.4568-2.81210.16021510.15072809100
2.8121-3.54190.16931380.15492824100
3.5419-29.0890.15961680.14062872100
Refinement TLS params.Method: refined / Origin x: 11.5455 Å / Origin y: -1.8412 Å / Origin z: 15.8777 Å
111213212223313233
T0.0878 Å2-0.0025 Å20.0002 Å2-0.0849 Å20.0028 Å2--0.0914 Å2
L0.5102 °2-0.0805 °2-0.0087 °2-0.4345 °20.0376 °2--0.5821 °2
S-0.0069 Å °-0.0236 Å °0.0053 Å °-0.0298 Å °0.0098 Å °0.0036 Å °0.0071 Å °0.0015 Å °0.0004 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA4 - 261
2X-RAY DIFFRACTION1allB262
3X-RAY DIFFRACTION1allD1 - 232
4X-RAY DIFFRACTION1allD233 - 258
5X-RAY DIFFRACTION1allC1

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