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- PDB-9hgp: Human Carbonic Anhydrase II in complex with a synthetic aromatic ... -

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Basic information

Entry
Database: PDB / ID: 9hgp
TitleHuman Carbonic Anhydrase II in complex with a synthetic aromatic oligoamide foldamer
Components
  • Carbonic anhydrase 2
  • Synthetic aromatic oligoamide foldamer
KeywordsLYASE / Human Carbonic Anhydrase 2 / Foldamer / Protein binding
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 / morphogenesis of an epithelium ...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 / morphogenesis of an epithelium / angiotensin-activated signaling pathway / positive regulation of synaptic transmission, GABAergic / 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 / 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
Carbonic anhydrase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
Synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsSigl, J.C. / Wang, L. / Huc, I.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Chem Sci / Year: 2025
Title: Structure-based design of an aromatic helical foldamer-protein interface.
Authors: Wang, L. / Douat, C. / Sigl, J. / Sai Reddy, P. / Fischer, L. / d'Estaintot, B.L. / Liu, Z. / Pophristic, V. / Yang, Y. / Zhang, Y. / Huc, I.
History
DepositionNov 20, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 15, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Carbonic anhydrase 2
D: Synthetic aromatic oligoamide foldamer
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,8105
Polymers32,5442
Non-polymers2663
Water6,449358
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: homology, 1:1 complex of HCA2 and synthetic AOF
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)81.682, 78.970, 46.116
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Space group name HallP22ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x+1/2,y+1/2,-z
#4: -x,-y,z

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Components

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Protein / Protein/peptide , 2 types, 2 molecules AD

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


Mass: 29273.062 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 BL21(DE3) (bacteria) / References: UniProt: P00918, carbonic anhydrase
#2: Protein/peptide Synthetic aromatic oligoamide foldamer


Mass: 3271.361 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Synthetic construct (others)

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Non-polymers , 4 types, 361 molecules

#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Feature type: SUBJECT OF INVESTIGATION / Comment: pH buffer*YM
#5: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Feature type: SUBJECT OF INVESTIGATION / Comment: DMSO, precipitant*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 358 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY

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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: 2.54 Å3/Da / Density % sol: 51.58 % / Description: colorless plates
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 25% PEG 4000, 200 mM Li2SO4, 100 mM Tris pH 8.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.87313 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Apr 14, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87313 Å / Relative weight: 1
ReflectionResolution: 2.05→17.17 Å / Num. obs: 19166 / % possible obs: 99.04 % / Redundancy: 4.4 % / Biso Wilson estimate: 25.15 Å2 / CC1/2: 0.96 / CC star: 0.99 / Rmerge(I) obs: 0.149 / Rpim(I) all: 0.075 / Rrim(I) all: 0.168 / Net I/σ(I): 7.2
Reflection shellResolution: 2.05→2.12 Å / Rmerge(I) obs: 0.492 / Num. unique obs: 3555 / CC1/2: 0.801 / R split: 0.2478 / Rrim(I) all: 0.5531 / % possible all: 97.2

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
CrysalisProdata reduction
CrysalisProdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.05→17.17 Å / SU ML: 0.2264 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 21.1626
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2309 1916 10 %
Rwork0.1708 17244 -
obs0.1767 19160 99.01 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 24.19 Å2
Refinement stepCycle: LAST / Resolution: 2.05→17.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2036 0 255 358 2649
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00782398
X-RAY DIFFRACTIONf_angle_d2.01823275
X-RAY DIFFRACTIONf_chiral_restr0.0593303
X-RAY DIFFRACTIONf_plane_restr0.0068412
X-RAY DIFFRACTIONf_dihedral_angle_d19.7364329
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.05-2.10.29371340.20561207X-RAY DIFFRACTION97.81
2.1-2.160.28341300.19241214X-RAY DIFFRACTION99.56
2.16-2.220.3131410.19421201X-RAY DIFFRACTION99.04
2.22-2.290.26441260.18011221X-RAY DIFFRACTION98.75
2.29-2.370.25351360.18511192X-RAY DIFFRACTION98.88
2.37-2.470.23251370.17441233X-RAY DIFFRACTION98.77
2.47-2.580.25461350.1861219X-RAY DIFFRACTION99.93
2.58-2.720.25491370.18491245X-RAY DIFFRACTION99.64
2.72-2.890.24771360.18481224X-RAY DIFFRACTION99.49
2.89-3.110.24051380.1841229X-RAY DIFFRACTION99.85
3.11-3.420.23081380.16541246X-RAY DIFFRACTION99.71
3.42-3.910.19861420.15031249X-RAY DIFFRACTION99.14
3.91-4.90.1841380.14181266X-RAY DIFFRACTION99.01
4.9-17.170.20881480.17181298X-RAY DIFFRACTION96.79

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