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- PDB-3oku: Human Carbonic Anhydrase II in complex with 2-Ethylestrone-3-O-su... -

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Basic information

Entry
Database: PDB / ID: 3oku
TitleHuman Carbonic Anhydrase II in complex with 2-Ethylestrone-3-O-sulfamate
ComponentsCarbonic anhydrase 2
KeywordsLYASE / mixed 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 / MIR / 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_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_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)29,9025
Polymers29,2891
Non-polymers6134
Water6,143341
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)42.168, 41.199, 71.548
Angle α, β, γ (deg.)90.00, 104.12, 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 / / 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
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, 345 molecules

#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.: 1 / 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: 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
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 341 / 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: 2.06 Å3/Da / Density % sol: 40.23 %
Crystal growTemperature: 298 K / 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
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jun 9, 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. obs: 40524 / % possible obs: 95.3 % / Observed criterion σ(I): 0 / Redundancy: 4.7 % / Biso Wilson estimate: 16.24 Å2 / Rsym value: 0.055 / Net I/σ(I): 28.4
Reflection shellResolution: 1.45→1.5 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.206 / Mean I/σ(I) obs: 6 / Rsym value: 0.206 / % possible all: 80.3

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIX1.6.3_467refinement
PDB_EXTRACT3.1data extraction
HKL-2000data reduction
HKL-2000data scaling
PHENIX1.6.3_467phasing
RefinementMethod to determine structure: MIR
Starting model: PDB ENTRY 2ILI

2ili


Resolution: 1.45→23.13 Å / Occupancy max: 1 / Occupancy min: 0 / SU ML: 0.18 / Isotropic thermal model: TLS / σ(F): 0 / Phase error: 13.89 / Stereochemistry target values: ML
Details: INDIVIDUAL COORDINATE AND ADP REFINEMENT, RIGID BODY, TLS, RIDING HYDROGEN, OCCUPANCY
RfactorNum. reflection% reflection
Rfree0.158 1999 4.97 %
Rwork0.141 --
obs0.142 40188 94.5 %
all-40524 -
Solvent computationShrinkage radii: 0.05 Å / VDW probe radii: 0.3 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 62.448 Å2 / ksol: 0.506 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--1.341 Å2-0 Å2-0.7559 Å2
2---0.095 Å20 Å2
3---1.4361 Å2
Refinement stepCycle: LAST / Resolution: 1.45→23.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2059 0 37 341 2437
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012375
X-RAY DIFFRACTIONf_angle_d1.4183271
X-RAY DIFFRACTIONf_dihedral_angle_d12.572926
X-RAY DIFFRACTIONf_chiral_restr0.083342
X-RAY DIFFRACTIONf_plane_restr0.008430
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.45-1.48590.35881110.39022054X-RAY DIFFRACTION73
1.4859-1.5260.30161360.28342631X-RAY DIFFRACTION91
1.526-1.57090.22381390.2122618X-RAY DIFFRACTION92
1.5709-1.62160.18271420.15082682X-RAY DIFFRACTION93
1.6216-1.67960.1541430.13982708X-RAY DIFFRACTION95
1.6796-1.74680.17761390.12842726X-RAY DIFFRACTION95
1.7468-1.82630.16741450.13432738X-RAY DIFFRACTION96
1.8263-1.92250.15971490.13322793X-RAY DIFFRACTION97
1.9225-2.04290.14571440.13652818X-RAY DIFFRACTION97
2.0429-2.20050.15281440.13332805X-RAY DIFFRACTION98
2.2005-2.42170.14471450.12212858X-RAY DIFFRACTION99
2.4217-2.77170.13511480.12742889X-RAY DIFFRACTION99
2.7717-3.49010.13141620.13162902X-RAY DIFFRACTION100
3.4901-23.13140.16191520.13872967X-RAY DIFFRACTION99
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)
10.0228-0.00510.00470.00630.00430.0231-0.070.1262-0.0425-0.0621-0.1287-0.4034-0.04560.2770.00010.1584-0.01360.04020.20680.01490.22767.9502-4.321310.8242
20.2433-0.1360.21780.4472-0.41620.8415-0.0997-0.2255-0.02330.10980.1043-0.0613-0.0040.0295-0.01260.10780.01420.01370.1513-0.00690.1092-4.0302-2.538127.5522
30.2561-0.01510.20040.2865-0.08130.26730.0669-0.03610.1005-0.0841-0.0270.0483-0.1546-0.01240.01180.14460.0023-0.01320.1180.00240.16-16.79026.784513.1098
40.4473-0.0686-0.00530.35310.01160.5564-0.0019-0.0031-0.0139-0.07320.00030.0211-0.0070.019900.1-0.0068-0.00320.08680.00020.0946-10.1025-3.468813.2198
50.1282-0.07630.0240.110.00990.0603-0.0558-0.44820.04550.18570.13340.03550.12690.0132-0.00150.14890.01140.01280.2437-0.00180.1303-11.7926-3.600634.4292
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESID 3:9)
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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