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- PDB-3okv: Human Carbonic Anhydrase II A65S, N67Q (CA IX mimic) bound with 2... -

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Basic information

Entry
Database: PDB / ID: 3okv
TitleHuman Carbonic Anhydrase II A65S, N67Q (CA IX mimic) bound with 2-Ethylestrone 3-O-sulfamate
ComponentsCarbonic anhydrase 2
KeywordsLYASE / Mixes alpha/beta fold / Reversible hydration of Carbon Dioxide to Bicarbonate
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-VZ4 / Carbonic anhydrase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.45 Å
AuthorsSippel, K.H. / Stander, B.A. / Robbins, A.H. / Tu, C.K. / Agbandje-McKenna, M. / Silverman, D.N. / Joubert, A.M. / McKenna, R.
Citation
Journal: LETT.DRUG DES.DISCOVERY / Year: 2011
Title: Characterization of Carbonic Anhydrase Isozyme Specific Inhibition by Sulfamated 2-Ethylestra Compounds
Authors: Sippel, K.H. / Stander, B.A. / Robbins, A.H. / Tu, C.K. / Agbandje-McKenna, M. / Silverman, D.N. / Joubert, A.M. / McKenna, R.
#1: Journal: Biochemistry / Year: 2010
Title: Structures of human carbonic anhydrase II/inhibitor complexes reveal a second binding site for steroidal and nonsteroidal inhibitors.
Authors: Cozier, G.E. / Leese, M.P. / Lloyd, M.D. / Baker, M.D. / Thiyagarajan, N. / Acharya, K.R. / Potter, B.V.
#2: Journal: Biochemistry / Year: 2009
Title: Design of a carbonic anhydrase IX active-site mimic to screen inhibitors for possible anticancer properties.
Authors: Genis, C. / Sippel, K.H. / Case, N. / Cao, W. / Avvaru, B.S. / Tartaglia, L.J. / Govindasamy, L. / Tu, C. / Agbandje-McKenna, M. / Silverman, D.N. / Rosser, C.J. / McKenna, R.
History
DepositionAug 25, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 6, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software
Revision 1.3Sep 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_ref_seq_dif / 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_ptnr2_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_ref_seq_dif.details / _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)30,2185
Polymers29,3191
Non-polymers8994
Water6,593366
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)42.263, 41.297, 72.397
Angle α, β, γ (deg.)90.00, 104.32, 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: 29319.086 Da / Num. of mol.: 1 / Mutation: A65S, N67Q
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-VZ4 / (9beta)-2-ethyl-17-oxoestra-1(10),2,4-trien-3-yl sulfamate


Mass: 377.498 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H27NO4S
#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.: 366 / 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: 41.09 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 1.4 M Sodium citrate, 100mM Tris, 7.5 mM 2-Ethylestrone 3-O-sulfamate, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jun 8, 2010 / Details: Osmic mirrors
RadiationMonochromator: Graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.45→50 Å / Num. all: 40167 / Num. obs: 40167 / % possible obs: 94 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.8 % / Rsym value: 0.051 / Net I/σ(I): 28.5
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsRsym valueDiffraction-ID% possible all
1.45-1.54.50.1817.970.181176.9
1.5-1.565.80.14412.20.144192.9
1.56-1.635.70.11414.30.114193.4
1.63-1.725.70.09215.50.092194.2
1.72-1.835.70.07419.40.074194.8
1.83-1.975.80.05927.10.059196.6
1.97-2.176.10.05130.70.051197.3
2.17-2.486.20.04932.30.049198.2
2.48-3.126.20.04733.40.047199.1
3.12-505.70.04630.80.046196.6

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIX1.6.3_467refinement
PDB_EXTRACT3.1data extraction
CrystalCleardata collection
HKL-2000data reduction
HKL-2000data scaling
PHENIX1.6.3_467phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2ili

2ili


Resolution: 1.45→28.704 Å / Occupancy max: 1 / Occupancy min: 0.2 / SU ML: 0.15 / Isotropic thermal model: TLS / σ(F): 0 / Phase error: 13.18 / Stereochemistry target values: ML
Details: Individual coordinate and ADP refinement, rigid body, TLS, riding hydrogen, occupancy
RfactorNum. reflection% reflection
Rfree0.147 2005 5.01 %
Rwork0.1316 --
obs0.1323 39985 92.22 %
all-40167 -
Solvent computationShrinkage radii: 0.41 Å / VDW probe radii: 0.6 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 53.33 Å2 / ksol: 0.455 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--1.07 Å2-0 Å20.1548 Å2
2---0.0194 Å20 Å2
3---1.0894 Å2
Refinement stepCycle: LAST / Resolution: 1.45→28.704 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2051 0 57 366 2474
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092453
X-RAY DIFFRACTIONf_angle_d1.3833391
X-RAY DIFFRACTIONf_dihedral_angle_d13.309974
X-RAY DIFFRACTIONf_chiral_restr0.079357
X-RAY DIFFRACTIONf_plane_restr0.008442
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.45-1.48390.35291020.31441586X-RAY DIFFRACTION55
1.4839-1.5240.2571200.22512516X-RAY DIFFRACTION85
1.524-1.56880.18341470.17582686X-RAY DIFFRACTION92
1.5688-1.61950.16851380.13752693X-RAY DIFFRACTION93
1.6195-1.67740.15241390.12972760X-RAY DIFFRACTION93
1.6774-1.74450.14661520.12812751X-RAY DIFFRACTION94
1.7445-1.82390.16161390.12562775X-RAY DIFFRACTION95
1.8239-1.920.15471520.12212800X-RAY DIFFRACTION96
1.92-2.04030.14851560.12712847X-RAY DIFFRACTION97
2.0403-2.19780.14621530.12982887X-RAY DIFFRACTION98
2.1978-2.41880.13011480.11962886X-RAY DIFFRACTION98
2.4188-2.76860.14441560.12272926X-RAY DIFFRACTION99
2.7686-3.48720.13151510.12352963X-RAY DIFFRACTION99
3.4872-28.70930.12851520.12812904X-RAY DIFFRACTION96
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.5855-0.3846-0.29620.37030.02290.0668-0.01650.0636-0.1752-0.0749-0.0752-0.2808-0.02240.09760.08880.1174-0.01920.05620.1833-0.00550.22856.6971-4.442911.5257
20.2325-0.26820.32360.6574-0.30750.6295-0.109-0.1824-0.00580.09470.0989-0.0789-0.0150.01390.00130.06740.01870.00090.118-0.00630.0603-4.154-2.526527.983
30.5125-0.03820.05160.09660.13540.33030.034-0.00420.1187-0.0769-0.0050.0561-0.1208-0.0375-0.01170.09820.00650.00050.06620.01870.1184-16.78137.297813.2276
40.4214-0.07720.00250.3705-0.07460.41580.00810.0057-0.0116-0.06730.00330.00190.00450.0081-0.0080.0708-0.0019-0.00180.06030.00620.0643-10.549-3.127613.6016
50.83360.0588-0.43170.5764-0.13880.2518-0.0609-0.22680.03310.12770.13990.04320.0528-0.0163-0.06940.08880.01940.0050.15790.00350.0657-11.1858-2.876834.6465
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESID 4:9)
2X-RAY DIFFRACTION2(CHAIN A AND RESID 10:45)
3X-RAY DIFFRACTION3(CHAIN A AND RESID 46:87)
4X-RAY DIFFRACTION4(CHAIN A AND RESID 88:251)
5X-RAY DIFFRACTION5(CHAIN A AND RESID 252:261)

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