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- PDB-3kwa: Polyamines inhibit carbonic anhydrases -

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Basic information

Entry
Database: PDB / ID: 3kwa
TitlePolyamines inhibit carbonic anhydrases
ComponentsCarbonic anhydrase 2
KeywordsLYASE / polyamines / carbonic anhydrase II / inhibition
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 / angiotensin-activated signaling pathway ...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 / angiotensin-activated signaling pathway / positive regulation of synaptic transmission, GABAergic / 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 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
: / SPERMINE / Carbonic anhydrase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsTemperini, C.
CitationJournal: J.Med.Chem. / Year: 2010
Title: Polyamines inhibit carbonic anhydrases by anchoring to the zinc-coordinated water molecule
Authors: Carta, F. / Temperini, C. / Innocenti, A. / Scozzafava, A. / Kaila, K. / Supuran, C.T.
History
DepositionDec 1, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 14, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Carbonic anhydrase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,7574
Polymers29,2891
Non-polymers4683
Water3,243180
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)41.430, 42.160, 72.250
Angle α, β, γ (deg.)90.00, 104.30, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 29289.062 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: The protein was purchased from Sigma-Aldrich. / Source: (natural) Homo sapiens (human) / References: UniProt: P00918, 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-HG / MERCURY (II) ION


Mass: 200.590 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Hg
#4: Chemical ChemComp-SPM / SPERMINE


Mass: 202.340 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H26N4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 180 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsNON SEQUENTIAL NUMBERING IS USED IN THIS ENTRY. THE NUMBER 126 IS SIMPLY SKIPPED.

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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: 2.09 Å3/Da / Density % sol: 41.08 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.8
Details: 50mM Tris-HCl pH 7.7-7.8, 2mM sodium 4-(hydroxymercury)benzoate, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SEALED TUBE / Type: OXFORD DIFFRACTION ENHANCE ULTRA / Wavelength: 1.54 Å
DetectorType: OXFORD SAPPHIRE CCD / Detector: CCD / Date: May 27, 2007
RadiationMonochromator: capillary / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2→20 Å / Num. obs: 16497 / % possible obs: 99 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 0 / Redundancy: 3.9 % / Rsym value: 0.15 / Net I/σ(I): 4.48 / Num. measured all: 65214
Reflection shellResolution: 2→2.1 Å / Redundancy: 3.6 % / Mean I/σ(I) obs: 1.25 / Num. unique all: 8624 / Rsym value: 0.4

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Processing

Software
NameVersionClassification
CrysalisProOxford Diffraction2006data collection
AMoREphasing
REFMAC5.2.0005refinement
CrysalisProOxford Diffraction2006data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1CA2

1ca2


Resolution: 2→12.09 Å / Cor.coef. Fo:Fc: 0.895 / Cor.coef. Fo:Fc free: 0.845 / SU B: 7.656 / SU ML: 0.206 / Cross valid method: THROUGHOUT / ESU R: 0.276 / ESU R Free: 0.221 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2858 823 5 %RANDOM
Rwork0.23336 ---
obs0.23607 15634 99.42 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 13.755 Å2
Baniso -1Baniso -2Baniso -3
1--0.11 Å20 Å20.09 Å2
2--0.24 Å20 Å2
3----0.08 Å2
Refinement stepCycle: LAST / Resolution: 2→12.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2039 0 16 180 2235
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0222119
X-RAY DIFFRACTIONr_angle_refined_deg1.7221.9522871
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.7475256
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.21924.69498
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.11715349
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.311157
X-RAY DIFFRACTIONr_chiral_restr0.1170.2299
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021623
X-RAY DIFFRACTIONr_nbd_refined0.2260.21071
X-RAY DIFFRACTIONr_nbtor_refined0.3070.21349
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1940.2190
X-RAY DIFFRACTIONr_metal_ion_refined0.0670.22
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2980.244
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1380.210
X-RAY DIFFRACTIONr_mcbond_it0.7291.51315
X-RAY DIFFRACTIONr_mcangle_it1.18522063
X-RAY DIFFRACTIONr_scbond_it1.8863932
X-RAY DIFFRACTIONr_scangle_it2.7024.5808
LS refinement shellResolution: 2→2.051 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.352 62 -
Rwork0.289 1115 -
obs--99.07 %

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