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- PDB-5thn: Crystal Structure of 2-Hydroxycyclohepta-2,4,6-triene-1-thione bo... -

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Basic information

Entry
Database: PDB / ID: 5thn
TitleCrystal Structure of 2-Hydroxycyclohepta-2,4,6-triene-1-thione bound to human carbonic anhydrase 2
ComponentsCarbonic anhydrase 2
KeywordsLYASE/LYASE INHIBITOR / Carbonic Anhydrase 2 / Complex / metalloenzyme inhibitor / LYASE-LYASE INHIBITOR complex
Function / homology
Function and homology information


positive regulation of dipeptide transmembrane transport / regulation of monoatomic anion transport / cyanamide hydratase / cyanamide hydratase activity / arylesterase activity / Reversible hydration of carbon dioxide / angiotensin-activated signaling pathway / Developmental Lineage of Pancreatic Ductal Cells / carbonic anhydrase / carbonate dehydratase activity ...positive regulation of dipeptide transmembrane transport / regulation of monoatomic anion transport / cyanamide hydratase / cyanamide hydratase activity / arylesterase activity / Reversible hydration of carbon dioxide / angiotensin-activated signaling pathway / Developmental Lineage of Pancreatic Ductal Cells / carbonic anhydrase / carbonate dehydratase activity / regulation of intracellular pH / carbon dioxide transport / Erythrocytes take up oxygen and release carbon dioxide / Erythrocytes take up carbon dioxide and release oxygen / apical part of cell / 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
2-hydroxycyclohepta-2,4,6-triene-1-thione / CITRIC ACID / MERCURIBENZOIC ACID / Carbonic anhydrase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.33 Å
AuthorsDick, B. / Cohen, S.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01 GM098435 United States
CitationJournal: J. Biol. Inorg. Chem. / Year: 2017
Title: Effect of donor atom identity on metal-binding pharmacophore coordination.
Authors: Dick, B.L. / Patel, A. / McCammon, J.A. / Cohen, S.M.
History
DepositionSep 29, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 26, 2017Provider: repository / Type: Initial release
Revision 1.1Jun 7, 2017Group: Database references
Revision 1.2Sep 20, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 4, 2023Group: 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
Revision 1.5Aug 12, 2026Group: Derived calculations / Structure summary
Category: pdbx_entry_details / pdbx_modification_feature ...pdbx_entry_details / pdbx_modification_feature / pdbx_nonpoly_atom_coordination / pdbx_nonpoly_atom_coordination_sphere / pdbx_nonpoly_atom_coordination_sphere_order / pdbx_struct_conn_angle / struct_conn
Description: Metalloprotein remediation / Provider: repository / Type: Remediation

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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)30,0996
Polymers29,2891
Non-polymers8105
Water3,747208
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area690 Å2
ΔGint-4 kcal/mol
Surface area11610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.982, 41.108, 71.670
Angle α, β, γ (deg.)90.00, 104.23, 90.00
Int Tables number4
Space group name H-MP1211

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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: 29289.062 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 (E. coli) / References: UniProt: P00918, carbonic anhydrase

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Non-polymers , 6 types, 213 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-MBO / MERCURIBENZOIC ACID


Mass: 321.703 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H5HgO2
#4: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-7CZ / 2-hydroxycyclohepta-2,4,6-triene-1-thione


Mass: 138.187 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H6OS
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 208 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.05 Å3/Da / Density % sol: 39.9 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8
Details: Ammonium Sulfate, Tris, pH 8.0 VAPOR DIFFUSION, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: ENRAF-NONIUS FR591 / Wavelength: 1.5478 Å
DetectorType: BRUKER SMART 6000 / Detector: CCD / Date: Aug 17, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5478 Å / Relative weight: 1
ReflectionResolution: 1.3→69.47 Å / Num. obs: 56931 / % possible obs: 96.8 % / Redundancy: 6.43 % / Rmerge(I) obs: 0.0217 / Net I/σ(I): 44.29
Reflection shellResolution: 1.3→1.33 Å / Redundancy: 1.16 % / Rmerge(I) obs: 0.343 / Num. unique all: 2256 / % possible all: 54.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
APEXdata collection
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3KS3

3ks3


Resolution: 1.33→40 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.955 / SU B: 0.905 / SU ML: 0.038 / Cross valid method: THROUGHOUT / ESU R: 0.057 / ESU R Free: 0.06 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20602 2631 4.8 %RANDOM
Rwork0.17575 ---
obs0.17717 51979 99.88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 12.35 Å2
Baniso -1Baniso -2Baniso -3
1-0.29 Å2-0 Å2-0.12 Å2
2---0.2 Å2-0 Å2
3----0.03 Å2
Refinement stepCycle: 1 / Resolution: 1.33→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2049 0 39 208 2296
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0270.0192261
X-RAY DIFFRACTIONr_bond_other_d0.0040.022074
X-RAY DIFFRACTIONr_angle_refined_deg2.4571.9563085
X-RAY DIFFRACTIONr_angle_other_deg1.3083.0024818
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5065278
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.00424.808104
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.43115368
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.808157
X-RAY DIFFRACTIONr_chiral_restr0.1580.2318
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.0212596
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02524
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_it1.4451.0081085
X-RAY DIFFRACTIONr_mcbond_other1.4451.0051084
X-RAY DIFFRACTIONr_mcangle_it2.0921.5111372
X-RAY DIFFRACTIONr_mcangle_other2.0921.5141373
X-RAY DIFFRACTIONr_scbond_it2.4411.2681176
X-RAY DIFFRACTIONr_scbond_other2.4411.2681175
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.6321.7961714
X-RAY DIFFRACTIONr_long_range_B_refined4.7269.2262709
X-RAY DIFFRACTIONr_long_range_B_other4.7259.2282710
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.33→1.365 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.25 200 -
Rwork0.245 3792 -
obs--99.63 %

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