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- PDB-5txy: Identification of a New Zinc Binding Chemotype of by Fragment Scr... -

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Basic information

Entry
Database: PDB / ID: 5txy
TitleIdentification of a New Zinc Binding Chemotype of by Fragment Screening on human carbonic anhydrase
ComponentsCarbonic anhydrase 2
KeywordsLYASE / human carbonic anhydrase / Zinc Binding Chemotype / crystal / crystallization
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 / arylesterase activity / regulation of chloride transport / Reversible hydration of carbon dioxide / angiotensin-activated signaling pathway ...positive regulation of cellular pH reduction / positive regulation of dipeptide transmembrane transport / regulation of monoatomic anion transport / secretion / cyanamide hydratase / cyanamide hydratase activity / arylesterase activity / regulation of chloride transport / Reversible hydration of carbon dioxide / angiotensin-activated signaling pathway / positive regulation of synaptic transmission, GABAergic / regulation of intracellular pH / morphogenesis of an epithelium / 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 II / Alpha carbonic anhydrase / 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 ...Carbonic Anhydrase II / Alpha carbonic anhydrase / 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 / Roll / Alpha Beta
Similarity search - Domain/homology
(5R)-5-phenyl-1,3-oxazolidine-2,4-dione / FORMIC ACID / Carbonic anhydrase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.206 Å
AuthorsRen, B. / Peat, T.S. / Poulsen, S.-A.
CitationJournal: J. Med. Chem. / Year: 2017
Title: Identification of a New Zinc Binding Chemotype by Fragment Screening.
Authors: Chrysanthopoulos, P.K. / Mujumdar, P. / Woods, L.A. / Dolezal, O. / Ren, B. / Peat, T.S. / Poulsen, S.A.
History
DepositionNov 17, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 30, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Carbonic anhydrase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,5784
Polymers29,2891
Non-polymers2893
Water7,837435
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)42.154, 41.410, 72.072
Angle α, β, γ (deg.)90.00, 104.17, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Carbonic anhydrase 2 / / Carbonate dehydratase II / Carbonic anhydrase C / CAC / Carbonic anhydrase II / CA-II


Mass: 29289.062 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CA2 / Production host: Escherichia coli (E. coli) / References: UniProt: P00918, carbonic anhydrase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-FMT / FORMIC ACID / Formic acid


Mass: 46.025 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH2O2
#4: Chemical ChemComp-7Q1 / (5R)-5-phenyl-1,3-oxazolidine-2,4-dione


Mass: 177.157 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H7NO3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 435 / Source method: isolated from a natural source / Formula: H2O

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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: 2.08 Å3/Da / Density % sol: 40.93 %
Crystal growTemperature: 280 K / Method: vapor diffusion, sitting drop
Details: 2.58 M ammonium sulfate, 0.1 M tris-chloride (pH 8.9)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.99 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 8, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99 Å / Relative weight: 1
ReflectionResolution: 1.206→40.871 Å / Num. obs: 71984 / % possible obs: 87.4 % / Redundancy: 6.4 % / Net I/σ(I): 12.8

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
Aimlessdata scaling
PHASESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.206→40.871 Å / SU ML: 0.11 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 17.07
RfactorNum. reflection% reflection
Rfree0.1748 1992 2.77 %
Rwork0.1589 --
obs0.1594 71970 96.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.206→40.871 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2039 0 17 435 2491
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0142244
X-RAY DIFFRACTIONf_angle_d1.5863065
X-RAY DIFFRACTIONf_dihedral_angle_d13.081853
X-RAY DIFFRACTIONf_chiral_restr0.082317
X-RAY DIFFRACTIONf_plane_restr0.009406
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.2064-1.23660.26831200.24734571X-RAY DIFFRACTION90
1.2366-1.270.25731460.22144864X-RAY DIFFRACTION95
1.27-1.30740.21481430.19534919X-RAY DIFFRACTION96
1.3074-1.34960.20731350.18684920X-RAY DIFFRACTION96
1.3496-1.39780.19931480.18014950X-RAY DIFFRACTION96
1.3978-1.45380.20471380.17114979X-RAY DIFFRACTION97
1.4538-1.520.19191440.16714975X-RAY DIFFRACTION97
1.52-1.60010.18971430.15355032X-RAY DIFFRACTION97
1.6001-1.70040.20361440.15155033X-RAY DIFFRACTION98
1.7004-1.83170.16171480.14665046X-RAY DIFFRACTION98
1.8317-2.0160.15311510.1485096X-RAY DIFFRACTION98
2.016-2.30770.1811390.14845110X-RAY DIFFRACTION99
2.3077-2.90730.17261480.15685181X-RAY DIFFRACTION100
2.9073-40.89430.14261450.14815302X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.44430.39030.84460.6579-0.42461.5876-0.05530.0503-0.2469-0.1693-0.0168-0.42960.12360.13120.06370.08430.00780.04780.1403-0.00330.186729.8385-4.301915.0739
21.53190.1705-0.28951.3845-0.10020.9654-0.0887-0.1660.04990.12730.0964-0.10610.02730.11350.00310.07560.0197-0.00850.1134-0.00370.074818.4055-2.872728.669
30.7736-0.45220.35091.0608-0.20290.92210.0606-0.0810.1326-0.11490.04220.0922-0.1811-0.2072-0.08430.1083-0.005-0.01620.13550.00420.11054.57444.102114.2718
40.70380.1335-0.12010.82620.0850.8636-0.0216-0.01020.0544-0.0640.02880.1189-0.0497-0.0275-0.00580.0787-0.0032-0.00380.0730.00350.08728.1914-0.293817.2338
50.57220.1372-0.06441.10630.29270.78170.01-0.02980.0414-0.0768-0.01220.0784-0.0555-0.0117-0.00750.07610.0029-0.00260.06960.00330.07119.14113.524317.7977
63.7231.8374-1.35912.6086-1.25612.6266-0.15720.4982-0.0748-0.54280.11040.13460.0759-0.28750.06440.2046-0.009-0.03490.1512-0.02030.10265.4635-6.13380.0162
71.02390.0118-0.16310.65360.02030.70060.03250.19060.0069-0.2237-0.00310.0852-0.0676-0.1486-0.01830.15020.0068-0.02190.11590.01310.09425.1232-0.30385.9687
80.3516-0.13280.02210.67420.14340.6486-0.0086-0.0419-0.0065-0.01450.01160.02050.0120.0039-0.00360.06480.00330.00150.07280.00130.076710.9114-1.463422.2911
91.61570.2323-0.61861.0632-0.56131.2803-0.0130.2311-0.2088-0.2952-0.0258-0.13250.00870.06620.01720.1806-0.00910.0260.1179-0.02350.089216.0095-10.50041.1043
100.8566-0.10590.44341.15540.54350.9555-0.013-0.1583-0.00290.02860.0872-0.05740.03210.1065-0.070.06580.00170.00660.0760.01560.075815.8435-5.965623.8872
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 5 through 19 )
2X-RAY DIFFRACTION2chain 'A' and (resid 20 through 39 )
3X-RAY DIFFRACTION3chain 'A' and (resid 40 through 70 )
4X-RAY DIFFRACTION4chain 'A' and (resid 71 through 115 )
5X-RAY DIFFRACTION5chain 'A' and (resid 116 through 153 )
6X-RAY DIFFRACTION6chain 'A' and (resid 154 through 166 )
7X-RAY DIFFRACTION7chain 'A' and (resid 167 through 189 )
8X-RAY DIFFRACTION8chain 'A' and (resid 190 through 218 )
9X-RAY DIFFRACTION9chain 'A' and (resid 219 through 237 )
10X-RAY DIFFRACTION10chain 'A' and (resid 238 through 260 )

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