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- PDB-3p5l: Human Carbonic Anhydrase complexed with sodium 4-cyano-4-phenylpi... -

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Basic information

Entry
Database: PDB / ID: 3p5l
TitleHuman Carbonic Anhydrase complexed with sodium 4-cyano-4-phenylpiperidine-1-carbodithioate
ComponentsCarbonic anhydrase 2
Keywordslyase/inhibitor / carbothioates / HCAII inhibitors / lyase-inhibitor complex
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 / 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 / arylesterase activity / regulation of chloride transport / Reversible hydration of carbon dioxide / angiotensin-activated signaling pathway / positive regulation of synaptic transmission, GABAergic / regulation of intracellular pH / morphogenesis of an epithelium / 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
4-cyano-4-phenylpiperidine-1-carbodithioic acid / Carbonic anhydrase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.498 Å
AuthorsAggarwal, M. / McKenna, R.
CitationJournal: Chem.Commun.(Camb.) / Year: 2012
Title: Dithiocarbamates: a new class of carbonic anhydrase inhibitors. Crystallographic and kinetic investigations.
Authors: Carta, F. / Aggarwal, M. / Maresca, A. / Scozzafava, A. / McKenna, R. / Supuran, C.T.
History
DepositionOct 8, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 19, 2011Provider: repository / Type: Initial release
Revision 1.1Jan 25, 2012Group: Database references
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_seq_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

Downloads & links

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Assembly

Deposited unit
A: Carbonic anhydrase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,6954
Polymers29,2891
Non-polymers4063
Water3,099172
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)42.325, 41.310, 72.169
Angle α, β, γ (deg.)90.000, 104.450, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#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) / Strain (production host): BL21 (DE3) Plyss / 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-IT5 / 4-cyano-4-phenylpiperidine-1-carbodithioic acid


Mass: 262.394 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H14N2S2
#4: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE / Dimethyl sulfoxide


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


Mass: 18.015 Da / Num. of mol.: 172 / Source method: isolated from a natural source / Formula: H2O

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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: 41.03 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 1.6M Sodium Citrate, 50mM Tris-Cl, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jul 16, 2010
RadiationMonochromator: VARIMAX OPTICS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.498→20 Å / Num. all: 39014 / Num. obs: 38468 / % possible obs: 98.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.4 % / Rmerge(I) obs: 0.067 / Χ2: 1.044 / Net I/σ(I): 17.8
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.498-1.553.20.37137361.07196.3
1.55-1.623.30.27637501.09196.9
1.62-1.693.30.20837981.07197.3
1.69-1.783.30.15237751.049198.1
1.78-1.893.40.11338371.005198.9
1.89-2.043.40.08738501.09199
2.04-2.243.50.07238781.037199.7
2.24-2.563.50.06539170.9991100
2.56-3.233.50.05839161.0431100
3.23-203.50.05840111.001199.9

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIX1.6.3_467refinement
PDB_EXTRACT3.1data extraction
CrystalCleardata collection
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.498→19.987 Å / Occupancy max: 1 / Occupancy min: 0.1 / FOM work R set: 0.9017 / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1898 1870 4.98 %RANDOM
Rwork0.1659 ---
obs0.1671 37517 96.02 %-
all-39072 --
Solvent computationShrinkage radii: 0.29 Å / VDW probe radii: 0.5 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 37.931 Å2 / ksol: 0.501 e/Å3
Displacement parametersBiso max: 58.15 Å2 / Biso mean: 17.0089 Å2 / Biso min: 7.69 Å2
Baniso -1Baniso -2Baniso -3
1--0.6737 Å2-0 Å20.1856 Å2
2---0.8993 Å20 Å2
3---1.5731 Å2
Refinement stepCycle: LAST / Resolution: 1.498→19.987 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2049 0 22 172 2243
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0122216
X-RAY DIFFRACTIONf_angle_d1.4383017
X-RAY DIFFRACTIONf_chiral_restr0.089313
X-RAY DIFFRACTIONf_plane_restr0.008390
X-RAY DIFFRACTIONf_dihedral_angle_d15.495840
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.498-1.55190.35711660.33883214338087
1.5519-1.61410.27621700.2313365353591
1.6141-1.68750.23741770.18253479365693
1.6875-1.77640.17171880.14523493368196
1.7764-1.88760.17281890.14133594378397
1.8876-2.03320.2111950.14913606380198
2.0332-2.23760.18281920.15413663385599
2.2376-2.56080.17711970.1573698389599
2.5608-3.22420.19591940.171437213915100
3.2242-19.98860.16692020.161738144016100
Refinement TLS params.Method: refined / Origin x: -9.7509 Å / Origin y: -1.7544 Å / Origin z: 15.9638 Å
111213212223313233
T0.0693 Å2-0.0013 Å20.001 Å2-0.066 Å20.0028 Å2--0.0702 Å2
L0.4481 °2-0.0755 °20.0234 °2-0.2844 °2-0.0362 °2--0.3985 °2
S-0.0069 Å °-0.041 Å °0.0131 Å °-0.0365 Å °0.0073 Å °0.0039 Å °0.0105 Å °-0.002 Å °0 Å °
Refinement TLS groupSelection details: Chain A

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