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- PDB-8q3u: Crystal structure of a fentanyl derivative in complex with human ... -

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Basic information

Entry
Database: PDB / ID: 8q3u
TitleCrystal structure of a fentanyl derivative in complex with human CA VII
ComponentsCarbonic anhydrase 7
KeywordsLYASE / Carbonic anhydrase / fentanyl derivative / metalloenzyme / complex
Function / homology
Function and homology information


positive regulation of cellular pH reduction / regulation of chloride transport / Reversible hydration of carbon dioxide / positive regulation of synaptic transmission, GABAergic / regulation of intracellular pH / carbonic anhydrase / carbonate dehydratase activity / neuron cellular homeostasis / zinc ion binding / cytosol / cytoplasm
Similarity search - Function
Carbonic anhydrase VII / 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-J8I / Carbonic anhydrase 7
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.1 Å
AuthorsAlterio, V. / Di Fiore, A. / De Simone, G.
Funding support Italy, 1items
OrganizationGrant numberCountry
Ministero dell Universita e della RicercaPRIN201744BN5T Italy
CitationJournal: Eur.J.Med.Chem. / Year: 2023
Title: Discovery of a novel series of potent carbonic anhydrase inhibitors with selective affinity for mu Opioid receptor for Safer and long-lasting analgesia.
Authors: Angeli, A. / Micheli, L. / Turnaturi, R. / Pasquinucci, L. / Parenti, C. / Alterio, V. / Di Fiore, A. / De Simone, G. / Monti, S.M. / Carta, F. / Di Cesare Mannelli, L. / Ghelardini, C. / Supuran, C.T.
History
DepositionAug 4, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 20, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Carbonic anhydrase 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,5915
Polymers30,9261
Non-polymers6654
Water3,081171
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area470 Å2
ΔGint-1 kcal/mol
Surface area11570 Å2
Unit cell
Length a, b, c (Å)66.965, 89.422, 44.267
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Carbonic anhydrase 7 / Carbonate dehydratase VII / Carbonic anhydrase VII / CA-VII


Mass: 30925.693 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CA7 / Production host: Escherichia coli (E. coli) / References: UniProt: P43166, 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-J8I / ~{N}-phenyl-~{N}-[1-[2-(4-sulfamoylphenyl)ethyl]piperidin-4-yl]propanamide


Mass: 415.549 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H29N3O3S / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 171 / Source method: isolated from a natural source / Formula: H2O
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: 2.14 Å3/Da / Density % sol: 42.6 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 19% (w/v) PEG 3350, 0.2 M ammonium acetate, 0.1 M TRIS-HCl

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 14, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.1→44.7 Å / Num. obs: 107799 / % possible obs: 99.7 % / Redundancy: 10.8 % / CC1/2: 0.995 / Net I/σ(I): 11.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Num. unique obsCC1/2CC starΧ2% possible all
1.1-1.125.951530.6870.9021.03796.4
1.12-1.146.752710.7640.9311.06299
1.14-1.167.553350.8160.9481.07499.5
1.16-1.188.953290.8440.9571.09299.6
1.18-1.219.853130.9010.9741.09999.7
1.21-1.2410.553500.9220.981.09999.7
1.24-1.2711.553290.9350.9831.09799.9
1.27-1.311.453710.9570.9891.0799.9
1.3-1.3412.153760.9710.9931.08799.9
1.34-1.3911.853580.9750.9941.078100
1.39-1.4411.553730.9810.9951.041100
1.44-1.4912.153690.9860.9971.065100
1.49-1.5611.854070.9890.9971.098100
1.56-1.6412.653890.9920.9981.047100
1.64-1.7512.154120.9930.9981.043100
1.75-1.881254330.9940.9991.089100
1.88-2.0711.754440.9940.9991.006100
2.07-2.3712.554770.9950.9991.09100
2.37-2.9912.155330.9960.9991.036100
2.99-44.711.957770.9930.9981.004100

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
SCALEPACKdata scaling
HKL-2000data reduction
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.1→44.7 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.978 / SU B: 0.826 / SU ML: 0.018 / Cross valid method: THROUGHOUT / ESU R: 0.027 / ESU R Free: 0.025 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.15322 1016 0.9 %RANDOM
Rwork0.14956 ---
obs0.1496 106719 99.61 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 15.03 Å2
Baniso -1Baniso -2Baniso -3
1--0.12 Å20 Å20 Å2
2---0.16 Å20 Å2
3---0.28 Å2
Refinement stepCycle: 1 / Resolution: 1.1→44.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2054 0 42 171 2267
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0132270
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171985
X-RAY DIFFRACTIONr_angle_refined_deg1.7711.6553101
X-RAY DIFFRACTIONr_angle_other_deg1.5381.5994642
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5875284
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.99321.579114
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.40515354
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.4191514
X-RAY DIFFRACTIONr_chiral_restr0.1150.2280
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.022594
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02504
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.1071.5071100
X-RAY DIFFRACTIONr_mcbond_other1.11099
X-RAY DIFFRACTIONr_mcangle_it1.5162.2681396
X-RAY DIFFRACTIONr_mcangle_other1.52122.231397
X-RAY DIFFRACTIONr_scbond_it1.3081.7691170
X-RAY DIFFRACTIONr_scbond_other1.3092.4631161
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.74111.821696
X-RAY DIFFRACTIONr_long_range_B_refined2.19918.1522442
X-RAY DIFFRACTIONr_long_range_B_other2.1617.8372407
X-RAY DIFFRACTIONr_rigid_bond_restr3.16932270
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.101→1.13 Å
RfactorNum. reflection% reflection
Rfree0.28 69 -
Rwork0.28 7555 -
obs--96.43 %

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