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- PDB-5m78: Human Carbonic Anhydrase II in complex with fragment-like inhibitor. -

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Basic information

Entry
Database: PDB / ID: 5m78
TitleHuman Carbonic Anhydrase II in complex with fragment-like inhibitor.
ComponentsCarbonic anhydrase 2
KeywordsLYASE / PROTEIN-LIGAND-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 / 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
MERCURIBENZOIC ACID / 2-HYDROXYBENZOIC ACID / Carbonic anhydrase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.077 Å
AuthorsGloeckner, S. / Heine, A. / Klebe, G.
CitationJournal: Biomolecules / Year: 2020
Title: A Proof-of-Concept Fragment Screening of a Hit-Validated 96-Compounds Library against Human Carbonic Anhydrase II.
Authors: Glockner, S. / Heine, A. / Klebe, G.
History
DepositionOct 27, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 20, 2017Provider: repository / Type: Initial release
Revision 1.1Apr 15, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name
Revision 1.2Jan 17, 2024Group: 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

Downloads & links

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Assembly

Deposited unit
A: Carbonic anhydrase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,4105
Polymers29,8071
Non-polymers6034
Water4,396244
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area950 Å2
ΔGint-40 kcal/mol
Surface area11420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.439, 41.423, 72.243
Angle α, β, γ (deg.)90.00, 104.75, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 1 molecules A

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


Mass: 29806.588 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: The first five residues (GSPEF) are residues from an expression tag.
Source: (gene. exp.) Homo sapiens (human) / Gene: CA2 / Plasmid: PGEX-4T1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Codon Plus / References: UniProt: P00918, carbonic anhydrase

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Non-polymers , 5 types, 248 molecules

#2: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE / Dimethyl sulfoxide


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-MBO / MERCURIBENZOIC ACID


Mass: 321.703 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H5HgO2
#5: Chemical ChemComp-SAL / 2-HYDROXYBENZOIC ACID / SALICYLIC ACID / Salicylic acid


Mass: 138.121 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H6O3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 244 / 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: 2.06 Å3/Da / Density % sol: 40.38 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.8
Details: Crystallization: 2 uL protein solution in 50 mM Tris, pH=7.8 mixed with 2 uL (NH4)2SO4, 100 mM Tris, pH=7.8, satured with PCMB and placed as hanging drop. Crystals appeared after a few days. ...Details: Crystallization: 2 uL protein solution in 50 mM Tris, pH=7.8 mixed with 2 uL (NH4)2SO4, 100 mM Tris, pH=7.8, satured with PCMB and placed as hanging drop. Crystals appeared after a few days. The crystal for data collection was soaked in 5 uL containing 35 % PEG 3350 (50 % w/v), 20 % NaCl (1 M), 25 % PEG 400, 10 % H2O, 10 % Ligandstock in DMSO (1 M)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.7999 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 6, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.7999 Å / Relative weight: 1
ReflectionResolution: 1.077→41.423 Å / Num. obs: 103054 / % possible obs: 98.3 % / Redundancy: 3.7 % / CC1/2: 0.998 / Rsym value: 0.066 / Net I/σ(I): 9.87
Reflection shellResolution: 1.077→1.14 Å / Redundancy: 3.64 % / Rmerge(I) obs: 0.399 / Mean I/σ(I) obs: 2.36 / CC1/2: 0.846 / % possible all: 95

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3KS3

3ks3


Resolution: 1.077→35.631 Å / SU ML: 0.08 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 12.11
RfactorNum. reflection% reflection
Rfree0.144 5153 5 %
Rwork0.1252 --
obs0.1261 103048 98.32 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.077→35.631 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2029 0 25 244 2298
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072341
X-RAY DIFFRACTIONf_angle_d0.9693208
X-RAY DIFFRACTIONf_dihedral_angle_d12.607863
X-RAY DIFFRACTIONf_chiral_restr0.081329
X-RAY DIFFRACTIONf_plane_restr0.007442
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.0775-1.08970.21941420.21062707X-RAY DIFFRACTION82
1.0897-1.10260.19851700.19033216X-RAY DIFFRACTION99
1.1026-1.1160.17991720.17813283X-RAY DIFFRACTION98
1.116-1.13010.19241700.16183223X-RAY DIFFRACTION99
1.1301-1.1450.1851720.15663265X-RAY DIFFRACTION98
1.145-1.16070.18321700.1513234X-RAY DIFFRACTION98
1.1607-1.17730.18681730.14983275X-RAY DIFFRACTION99
1.1773-1.19480.16871700.14283236X-RAY DIFFRACTION98
1.1948-1.21350.15521720.14023271X-RAY DIFFRACTION99
1.2135-1.23340.14791720.1383261X-RAY DIFFRACTION99
1.2334-1.25470.14481710.1353254X-RAY DIFFRACTION99
1.2547-1.27750.1561700.13063239X-RAY DIFFRACTION99
1.2775-1.30210.14531730.11993275X-RAY DIFFRACTION99
1.3021-1.32870.12431740.11543310X-RAY DIFFRACTION99
1.3287-1.35750.12781710.11093253X-RAY DIFFRACTION99
1.3575-1.38910.13511740.1153303X-RAY DIFFRACTION99
1.3891-1.42390.11661720.11373275X-RAY DIFFRACTION99
1.4239-1.46240.13361740.10843305X-RAY DIFFRACTION100
1.4624-1.50540.14061750.11273308X-RAY DIFFRACTION99
1.5054-1.5540.14041710.10593258X-RAY DIFFRACTION99
1.554-1.60950.14071740.10563311X-RAY DIFFRACTION99
1.6095-1.6740.12181730.10413284X-RAY DIFFRACTION100
1.674-1.75020.12431760.10753336X-RAY DIFFRACTION99
1.7502-1.84240.12971740.10933306X-RAY DIFFRACTION99
1.8424-1.95780.13561720.11043279X-RAY DIFFRACTION99
1.9578-2.1090.11071740.11293307X-RAY DIFFRACTION99
2.109-2.32120.13221720.11683263X-RAY DIFFRACTION98
2.3212-2.6570.13531750.12233326X-RAY DIFFRACTION99
2.657-3.34710.15221750.1333332X-RAY DIFFRACTION99
3.3471-35.650.16041800.13633400X-RAY DIFFRACTION98

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