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- PDB-6ugn: Human Carbonic Anhydrase 2 complexed with SB4-205 -

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Basic information

Entry
Database: PDB / ID: 6ugn
TitleHuman Carbonic Anhydrase 2 complexed with SB4-205
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 / cyanamide hydratase activity / regulation of chloride transport / arylesterase activity / Reversible hydration of carbon dioxide / positive regulation of synaptic transmission, GABAergic ...positive regulation of cellular pH reduction / positive regulation of dipeptide transmembrane transport / regulation of monoatomic anion transport / secretion / cyanamide hydratase / cyanamide hydratase activity / regulation of chloride transport / arylesterase activity / Reversible hydration of carbon dioxide / positive regulation of synaptic transmission, GABAergic / angiotensin-activated signaling pathway / morphogenesis of an epithelium / 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 / one-carbon metabolic process / apical part of cell / myelin sheath / extracellular exosome / zinc ion binding / plasma membrane / cytosol / cytoplasm
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-Q77 / Carbonic anhydrase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.406 Å
AuthorsMurray, A.B. / Supuran, C.T. / 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)29,4514
Polymers28,9331
Non-polymers5183
Water3,603200
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area11790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.471, 41.481, 71.830
Angle α, β, γ (deg.)90.000, 104.490, 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-Q77 / 5,7-dimethyl-1lambda~6~,2,4-benzothiadiazine-1,1,3(2H,4H)-trione


Mass: 226.252 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H10N2O3S / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 200 / 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: 2.12 Å3/Da / Density % sol: 41.91 %
Crystal growTemperature: 298 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: 1.406→34.77 Å / Num. obs: 45791 / % possible obs: 97.1 % / Redundancy: 6.8 % / Biso Wilson estimate: 12.3 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.06 / Rpim(I) all: 0.025 / Rrim(I) all: 0.065 / Net I/σ(I): 18
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
1.41-1.4360.5351300621720.8820.2360.5863.193.5
7.7-34.776.10.03719093150.9990.0150.0441.698.4

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Processing

Software
NameVersionClassification
Aimless0.5.32data scaling
PHENIX1.11.1_2575refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
PHENIX1.11.1_2575phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3KS3

3ks3


Resolution: 1.406→29.203 Å / SU ML: 0.12 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 16.39
RfactorNum. reflection% reflection
Rfree0.1733 2277 4.97 %
Rwork0.1505 --
obs0.1516 45772 96.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 79.54 Å2 / Biso mean: 18.6674 Å2 / Biso min: 6.56 Å2
Refinement stepCycle: final / Resolution: 1.406→29.203 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2049 0 49 200 2298
Biso mean--20.21 24.81 -
Num. residues----257
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082149
X-RAY DIFFRACTIONf_angle_d1.1092925
X-RAY DIFFRACTIONf_chiral_restr0.082300
X-RAY DIFFRACTIONf_plane_restr0.008376
X-RAY DIFFRACTIONf_dihedral_angle_d14.803778
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.4065-1.4370.25731260.2367261494
1.437-1.47050.20291340.1998263595
1.4705-1.50720.22411250.1757269496
1.5072-1.5480.18441360.1633265295
1.548-1.59350.18311130.1573271596
1.5935-1.6450.1651130.1564270396
1.645-1.70380.19271390.1541268096
1.7038-1.7720.17421550.1525269996
1.772-1.85260.17991850.1433268597
1.8526-1.95020.16481510.1372268797
1.9502-2.07240.1621600.1368273998
2.0724-2.23240.16651460.1386273697
2.2324-2.45690.16311480.1418277199
2.4569-2.81220.1721550.1488277998
2.8122-3.54210.20131280.1577282399
3.5421-29.2030.14931630.1446288399
Refinement TLS params.Method: refined / Origin x: 11.7867 Å / Origin y: -1.2652 Å / Origin z: 15.9206 Å
111213212223313233
T0.0726 Å2-0.0028 Å20.0001 Å2-0.0714 Å20.0051 Å2--0.0795 Å2
L0.5316 °2-0.119 °2-0.0199 °2-0.3843 °2-0.0509 °2--0.6447 °2
S-0.0038 Å °-0.0025 Å °0.0254 Å °-0.0091 Å °0.0186 Å °0.0044 Å °0.008 Å °0.0014 Å °0.0032 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA4 - 261
2X-RAY DIFFRACTION1allB262
3X-RAY DIFFRACTION1allD1 - 202
4X-RAY DIFFRACTION1allC1 - 2

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