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- PDB-6sbm: Human Carbonic Anhydrase II in complex with 4-(pentyloxy)benzenes... -

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Basic information

Entry
Database: PDB / ID: 6sbm
TitleHuman Carbonic Anhydrase II in complex with 4-(pentyloxy)benzenesulfonamide
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
(4-CARBOXYPHENYL)(CHLORO)MERCURY / CITRATE ANION / 4-pentoxybenzenesulfonamide / Carbonic anhydrase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 0.95 Å
AuthorsGloeckner, S. / Ngo, K. / Heine, A. / Klebe, G.
CitationJournal: To Be Published
Title: Human Carbonic Anhydrase II in complex with 4-(pentyloxy)benzenesulfonamide
Authors: Gloeckner, S. / Ngo, K. / Heine, A. / Klebe, G.
History
DepositionJul 21, 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)31,0299
Polymers29,8071
Non-polymers1,2228
Water4,161231
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area860 Å2
ΔGint-13 kcal/mol
Surface area11500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.348, 41.603, 71.968
Angle α, β, γ (deg.)90.000, 104.243, 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 , 7 types, 239 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-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-L4W / 4-pentoxybenzenesulfonamide


Mass: 243.323 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H17NO3S / Feature type: SUBJECT OF INVESTIGATION
#6: 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
#7: Chemical ChemComp-FLC / CITRATE ANION


Mass: 189.100 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H5O7
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 231 / 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: 2.06 Å3/Da / Density % sol: 40.42 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.8
Details: Sodium citrate 1.4 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: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 23, 2018
RadiationMonochromator: Si(111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 0.949→41.603 Å / Num. obs: 147595 / % possible obs: 96.4 % / Redundancy: 3.98 % / Biso Wilson estimate: 8.26 Å2 / CC1/2: 0.998 / Rsym value: 0.055 / Net I/σ(I): 12.05
Reflection shellResolution: 0.95→1.01 Å / Mean I/σ(I) obs: 2.48 / Num. unique obs: 22749 / CC1/2: 0.873 / Rsym value: 0.333 / % possible all: 92.2

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Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3KS3

3ks3


Resolution: 0.95→39.93 Å / SU ML: 0.0635 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 10.215
RfactorNum. reflection% reflectionSelection details
Rfree0.1284 7378 5 %Random selection of 5 %
Rwork0.1173 ---
obs0.1178 147562 96.43 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 12.14 Å2
Refinement stepCycle: LAST / Resolution: 0.95→39.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2011 0 58 231 2300
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00622755
X-RAY DIFFRACTIONf_angle_d0.94773810
X-RAY DIFFRACTIONf_chiral_restr0.0882379
X-RAY DIFFRACTIONf_plane_restr0.007543
X-RAY DIFFRACTIONf_dihedral_angle_d14.75381028
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
0.95-0.960.23462140.20064069X-RAY DIFFRACTION83.39
0.96-0.970.19882340.17924452X-RAY DIFFRACTION93.44
0.97-0.980.18392420.15924592X-RAY DIFFRACTION94.67
0.98-10.16882390.15244538X-RAY DIFFRACTION95.25
1-1.010.14482410.14434591X-RAY DIFFRACTION94.76
1.01-1.020.15122420.13114598X-RAY DIFFRACTION95.18
1.02-1.040.15092450.13124638X-RAY DIFFRACTION95.43
1.04-1.050.12892380.1184530X-RAY DIFFRACTION94.72
1.05-1.070.11652440.10574634X-RAY DIFFRACTION96.16
1.07-1.090.10562460.09884661X-RAY DIFFRACTION96.12
1.09-1.110.10942440.09864630X-RAY DIFFRACTION96.53
1.11-1.130.10342460.09274671X-RAY DIFFRACTION96.13
1.13-1.150.10642430.08924641X-RAY DIFFRACTION96.18
1.15-1.170.10922440.08994630X-RAY DIFFRACTION95.89
1.17-1.20.0942440.08974642X-RAY DIFFRACTION96.2
1.2-1.220.10912480.08914705X-RAY DIFFRACTION97.4
1.22-1.250.10442470.09254697X-RAY DIFFRACTION97.34
1.25-1.290.11592480.09324716X-RAY DIFFRACTION97.6
1.29-1.330.10952500.09594737X-RAY DIFFRACTION97.84
1.33-1.370.12542500.09924758X-RAY DIFFRACTION98.1
1.37-1.420.12052470.09884686X-RAY DIFFRACTION96.99
1.42-1.470.12012490.09864728X-RAY DIFFRACTION98.03
1.47-1.540.11952530.09794816X-RAY DIFFRACTION98.93
1.54-1.620.11942540.0994820X-RAY DIFFRACTION99.16
1.62-1.730.10862530.10624816X-RAY DIFFRACTION99.12
1.73-1.860.12772530.11314807X-RAY DIFFRACTION98.73
1.86-2.050.12072500.11674744X-RAY DIFFRACTION97.42
2.05-2.340.11972550.12024851X-RAY DIFFRACTION99.15
2.34-2.950.13822560.13864863X-RAY DIFFRACTION98.94
2.95-39.930.15212590.14034923X-RAY DIFFRACTION98.22

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