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- PDB-6h29: HUMAN CARBONIC ANHYDRASE II IN COMPLEX WITH BENZYL CARBAMATE -

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Basic information

Entry
Database: PDB / ID: 6h29
TitleHUMAN CARBONIC ANHYDRASE II IN COMPLEX WITH BENZYL CARBAMATE
ComponentsCarbonic anhydrase 2
KeywordsLYASE / BENZYL CARBAMATE / INHIBITOR COMPLEX / HUMAN CARBONIC ANHYDRASE II
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
(phenylmethyl) carbamate / Carbonic anhydrase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 1.46 Å
AuthorsAlterio, V. / De Simone, G.
CitationJournal: Chem. Commun. (Camb.) / Year: 2018
Title: Inhibition of carbonic anhydrases by a substrate analog: benzyl carbamate directly coordinates the catalytic zinc ion mimicking bicarbonate binding.
Authors: De Simone, G. / Angeli, A. / Bozdag, M. / Supuran, C.T. / Winum, J.Y. / Monti, S.M. / Alterio, V.
History
DepositionJul 13, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 5, 2018Provider: repository / Type: Initial release
Revision 1.1Sep 19, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Oct 24, 2018Group: Data collection / Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain
Revision 1.3Jan 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)29,5063
Polymers29,2891
Non-polymers2172
Water4,738263
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area12030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.323, 41.586, 71.818
Angle α, β, γ (deg.)90.000, 104.380, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Carbonic anhydrase 2 / / Carbonic anhydrase II


Mass: 29289.062 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli BL21(DE3) (bacteria) / 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-FK8 / (phenylmethyl) carbamate / Benzyl carbamate


Mass: 151.163 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H9NO2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 263 / 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: 2.09 Å3/Da / Density % sol: 41.16 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 1.3 M sodium citrate, 60 mM Tris-HCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54178 Å
DetectorType: RIGAKU SATURN 944 / Detector: CCD / Date: Oct 5, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 1.46→28.8 Å / Num. obs: 41125 / % possible obs: 97.3 % / Redundancy: 4.6 % / Rmerge(I) obs: 0.046 / Rpim(I) all: 0.02 / Rrim(I) all: 0.051 / Χ2: 1.024 / Net I/av σ(I): 25.6 / Net I/σ(I): 32
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.46-1.492.10.19415800.9280.1470.2450.93874.7
1.49-1.5130.18919100.9530.1210.2260.97992
1.51-1.543.30.17219330.9610.1050.2031.02792.8
1.54-1.573.40.15320320.970.0930.181.03596.2
1.57-1.613.50.13820120.9780.0820.1611.09996.3
1.61-1.643.50.12520480.9790.0740.1461.0898.1
1.64-1.693.60.11920940.9810.0690.1381.04599.1
1.69-1.733.70.120960.9890.0570.1161.03199.5
1.73-1.783.90.09320680.990.0520.1071.07899.3
1.78-1.8440.0821250.9930.0440.0921.02899.6
1.84-1.914.20.06920850.9950.0370.0781.00399.7
1.91-1.984.30.06221230.9960.0330.0711.0899.9
1.98-2.074.50.05420960.9970.0280.0611.073100
2.07-2.184.60.0521180.9970.0260.0560.964100
2.18-2.324.90.05121160.9970.0250.0560.95100
2.32-2.55.50.06221280.9960.0280.0691.067100
2.5-2.755.80.05721070.9960.0250.0621.02799.8
2.75-3.156.10.04521140.9980.0190.0481.07799.3
3.15-3.967.50.03821330.9990.0140.0410.93799
3.96-28.89.20.03322070.9990.0110.0351.00999.6

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
CNSrefinement
PDB_EXTRACT3.24data extraction
HKL-2000data reduction
CNSphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 6EQU

6equ


Resolution: 1.46→28.8 Å / Cross valid method: FREE R-VALUE / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.1842 948 2.2 %random
Rwork0.1691 ---
obs-40053 94.8 %-
Solvent computationBsol: 42.1998 Å2
Displacement parametersBiso max: 40.28 Å2 / Biso mean: 12.2262 Å2 / Biso min: 2.52 Å2
Baniso -1Baniso -2Baniso -3
1--0.503 Å2-0 Å2-0.363 Å2
2--1.257 Å20 Å2
3----0.753 Å2
Refinement stepCycle: final / Resolution: 1.46→28.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2072 0 12 263 2347
Biso mean--16.41 21.51 -
Num. residues----260
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_angle_d1.545
X-RAY DIFFRACTIONc_mcbond_it1.1211.5
X-RAY DIFFRACTIONc_scbond_it1.9042
X-RAY DIFFRACTIONc_mcangle_it1.7422
X-RAY DIFFRACTIONc_scangle_it2.7272.5
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.46-1.510.2143750.21163170324577.4
1.51-1.570.1985980.18413656375489.4
1.57-1.640.1789780.17253800387893
1.64-1.730.1455880.16153950403895.8
1.73-1.840.1929900.1683966405696.3
1.84-1.980.21391230.16584017414098.1
1.98-2.180.1923920.16724108420099.6
2.18-2.50.1911110.16954089420099.1
2.5-3.140.1859930.17824115420899.2
3.14-28.80.16351000.15844234433499.5

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