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- PDB-3oy0: Human Carbonic Anhydrase II complexed with 1-(4-(4-(2-(ISOPROPYLS... -

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Basic information

Entry
Database: PDB / ID: 3oy0
TitleHuman Carbonic Anhydrase II complexed with 1-(4-(4-(2-(ISOPROPYLSULFONYL)PHENYLAMINO)-1H-PYRROLO[2,3-B]PYRIDIN-6-YLAMINO)-3-METHOXYPHENYL)PIPERIDIN-4-OL
ComponentsCarbonic anhydrase 2
Keywordslyase/lyase inhibitor / Benzene Sulfonamide / drug interaction / lyase-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
Chem-OY0 / Carbonic anhydrase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsAggarwal, M. / McKenna, R.
CitationJournal: J.Med.Chem. / Year: 2011
Title: Anticonvulsant 4-aminobenzenesulfonamide derivatives with branched-alkylamide moieties: X-ray crystallography and inhibition studies of human carbonic anhydrase isoforms I, II, VII, and XIV.
Authors: Hen, N. / Bialer, M. / Yagen, B. / Maresca, A. / Aggarwal, M. / Robbins, A.H. / McKenna, R. / Scozzafava, A. / Supuran, C.T.
History
DepositionSep 22, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 10, 2011Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2017Group: Refinement description / Category: software
Revision 1.2Sep 6, 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_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_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.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

Downloads & links

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Assembly

Deposited unit
A: Carbonic anhydrase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,8375
Polymers29,2891
Non-polymers5484
Water3,189177
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)42.235, 41.331, 72.028
Angle α, β, γ (deg.)90.000, 104.150, 90.000
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 / / 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 genetically manipulated source
Details: Purified using affinity chromatography / 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

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Non-polymers , 5 types, 181 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-OY0 / (2S)-2-tert-butyl-N-(4-sulfamoylphenyl)pentanamide


Mass: 312.428 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H24N2O3S
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: 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
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 177 / 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: 2.08 Å3/Da / Density % sol: 40.9 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 1.6M Sodium Citrate, 50mM Tris-Cl, detergent (Tween20), 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: Aug 20, 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: 1.6→50 Å / Num. all: 32101 / Num. obs: 28795 / % possible obs: 89.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.5 % / Rmerge(I) obs: 0.077 / Χ2: 0.989 / Net I/σ(I): 38
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.6-1.662.40.15928341.105189.5
1.66-1.722.40.13128851.02190.4
1.72-1.82.40.10928701.049190.7
1.8-1.92.50.09429271191.2
1.9-2.022.40.08529260.952191.7
2.02-2.172.50.0829370.937191.9
2.17-2.392.50.07329060.929191
2.39-2.742.60.07129010.993190.4
2.74-3.452.70.07528960.942189.1
3.45-502.80.07727130.98182

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIX1.6.3_467refinement
PDB_EXTRACT3.1data extraction
CrystalCleardata collection
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3KS3

3ks3


Resolution: 1.6→20.666 Å / Occupancy max: 1 / Occupancy min: 0.1 / FOM work R set: 0.906 / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1924 1432 5.01 %RANDOM
Rwork0.156 ---
obs0.1578 28574 89.12 %-
all-32101 --
Solvent computationShrinkage radii: 0.29 Å / VDW probe radii: 0.5 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40.702 Å2 / ksol: 0.48 e/Å3
Displacement parametersBiso max: 80.68 Å2 / Biso mean: 20.6883 Å2 / Biso min: 6.75 Å2
Baniso -1Baniso -2Baniso -3
1-1.2669 Å2-0 Å2-0.8337 Å2
2---2.3233 Å20 Å2
3---1.0564 Å2
Refinement stepCycle: LAST / Resolution: 1.6→20.666 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2049 0 32 177 2258
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0132193
X-RAY DIFFRACTIONf_angle_d1.4742984
X-RAY DIFFRACTIONf_chiral_restr0.092310
X-RAY DIFFRACTIONf_plane_restr0.008385
X-RAY DIFFRACTIONf_dihedral_angle_d14.494823
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 (%)
1.6-1.65690.32441410.26412614275587
1.6569-1.72320.27781440.21142702284689
1.7232-1.80160.24341370.16972703284090
1.8016-1.89650.18791460.13982750289690
1.8965-2.01520.17191440.13342766291091
2.0152-2.17070.18421500.13912776292692
2.1707-2.38880.18031430.1452757290091
2.3888-2.73380.18721460.14582752289890
2.7338-3.44180.17791410.15012750289189
3.4418-20.66720.18691400.16522572271282
Refinement TLS params.Method: refined / Origin x: -9.395 Å / Origin y: -1.8087 Å / Origin z: 15.8964 Å
111213212223313233
T0.0852 Å2-0.0054 Å20.0001 Å2-0.0823 Å2-0.0006 Å2--0.0862 Å2
L0.2842 °2-0.0909 °20.0188 °2-0.1883 °2-0.0391 °2--0.2208 °2
S-0.0018 Å °-0.0302 Å °0.0068 Å °-0.0217 Å °0.0039 Å °0.0202 Å °0.0138 Å °0.0029 Å °-0.0005 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA4 - 261
2X-RAY DIFFRACTION1allA1 - 439
3X-RAY DIFFRACTION1all262
4X-RAY DIFFRACTION1all1
5X-RAY DIFFRACTION1allA400
6X-RAY DIFFRACTION1allA1 - 440
7X-RAY DIFFRACTION1allA3092

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