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- PDB-6sdh: Human Carbonic Anhydrase II in complex with an inhibitor soaked a... -

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Basic information

Entry
Database: PDB / ID: 6sdh
TitleHuman Carbonic Anhydrase II in complex with an inhibitor soaked at a concentration of 5 mM
ComponentsCarbonic anhydrase 2
KeywordsLYASE / Inhibitor / complex / CO2 conversion
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-0VV / (4-CARBOXYPHENYL)(CHLORO)MERCURY / : / Carbonic anhydrase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.04 Å
AuthorsGloeckner, S. / Haake, M. / Heine, A. / Klebe, G.
CitationJournal: To Be Published
Title: Human Carbonic Anhydrase II in complex with an inhibitor soaked at a concentration of 5 mM
Authors: Gloeckner, S. / Haake, M. / Heine, A. / Klebe, G.
History
DepositionJul 27, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 26, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 24, 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)30,7346
Polymers29,8071
Non-polymers9285
Water2,864159
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area670 Å2
ΔGint-29 kcal/mol
Surface area10990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.298, 41.739, 72.337
Angle α, β, γ (deg.)90.000, 104.106, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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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 5 amino acids (GSPEF) are remnants of 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 , 6 types, 164 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#4: Chemical ChemComp-BE7 / (4-CARBOXYPHENYL)(CHLORO)MERCURY / P-CHLOROMERCURIBENZOIC ACID


Mass: 357.156 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H5ClHgO2 / Comment: protease inhibitor*YM
#5: Chemical ChemComp-HG / MERCURY (II) ION


Mass: 200.590 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Hg
#6: Chemical ChemComp-0VV / N-[(2E)-3,4-dihydroquinazolin-2(1H)-ylidene]sulfuric diamide


Mass: 226.256 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H10N4O2S / Feature type: SUBJECT OF INVESTIGATION
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 159 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.08 Å3/Da / Density % sol: 40.89 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.8
Details: Ammonium sulfate 2.7 M, TRIS 0.1 M, saturated with para-Chloromercuribenzoic acid

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.97625 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 19, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 1.039→41.739 Å / Num. obs: 112924 / % possible obs: 95.9 % / Redundancy: 3.5 % / Biso Wilson estimate: 10.75 Å2 / CC1/2: 0.989 / Rsym value: 0.083 / Net I/σ(I): 10.56
Reflection shellResolution: 1.04→1.1 Å / Redundancy: 2.89 % / Mean I/σ(I) obs: 4.26 / Num. unique obs: 15400 / CC1/2: 0.967 / Rsym value: 0.153 / % possible all: 81.1

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3KS3

3ks3


Resolution: 1.04→39.9 Å / SU ML: 0.0525 / Cross valid method: FREE R-VALUE / σ(F): 1.42 / Phase error: 10.8217
RfactorNum. reflection% reflectionSelection details
Rfree0.1475 5647 5 %Random selection of 5 %
Rwork0.1311 ---
obs0.1319 112922 95.93 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 14.88 Å2
Refinement stepCycle: LAST / Resolution: 1.04→39.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1986 0 31 159 2176
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00592409
X-RAY DIFFRACTIONf_angle_d1.01953317
X-RAY DIFFRACTIONf_chiral_restr0.0786346
X-RAY DIFFRACTIONf_plane_restr0.0072457
X-RAY DIFFRACTIONf_dihedral_angle_d11.9402878
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.04-1.050.18731180.16442231X-RAY DIFFRACTION59.97
1.05-1.060.15981410.13652689X-RAY DIFFRACTION71.99
1.06-1.080.14691590.12343021X-RAY DIFFRACTION82.02
1.08-1.090.14361840.10853498X-RAY DIFFRACTION94.8
1.09-1.10.12011950.1063699X-RAY DIFFRACTION99.57
1.1-1.120.12451940.10223674X-RAY DIFFRACTION99.56
1.12-1.140.11271940.09953685X-RAY DIFFRACTION99.41
1.14-1.150.12321950.09833710X-RAY DIFFRACTION99.41
1.15-1.170.10821920.09843652X-RAY DIFFRACTION98.59
1.17-1.190.12691890.09883587X-RAY DIFFRACTION96.92
1.19-1.210.12051950.09753705X-RAY DIFFRACTION99.62
1.21-1.230.12951950.09993701X-RAY DIFFRACTION99.74
1.23-1.260.11641950.10263720X-RAY DIFFRACTION99.67
1.26-1.280.12291940.10163681X-RAY DIFFRACTION99.26
1.28-1.310.13141930.09623661X-RAY DIFFRACTION98.87
1.31-1.340.11011910.09953640X-RAY DIFFRACTION98.28
1.34-1.370.12251920.09973650X-RAY DIFFRACTION98.21
1.37-1.410.11511960.09783725X-RAY DIFFRACTION99.29
1.41-1.450.12621940.1013674X-RAY DIFFRACTION98.98
1.45-1.50.12821930.09943660X-RAY DIFFRACTION98.92
1.5-1.550.10911940.13705X-RAY DIFFRACTION98.73
1.55-1.610.12451930.10073662X-RAY DIFFRACTION98.52
1.61-1.690.12371920.10943644X-RAY DIFFRACTION97.63
1.69-1.780.12471940.11153695X-RAY DIFFRACTION98.78
1.78-1.890.11341950.11443687X-RAY DIFFRACTION98.85
1.89-2.030.13561950.11813715X-RAY DIFFRACTION98.84
2.03-2.240.13341940.12633682X-RAY DIFFRACTION98.38
2.24-2.560.14591950.13453699X-RAY DIFFRACTION98.63
2.56-3.230.17421970.15283743X-RAY DIFFRACTION98.87
3.23-39.90.20911990.19193780X-RAY DIFFRACTION97.5

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