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- PDB-5fl6: Three dimensional structure of human carbonic anhydrase IX in com... -

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Basic information

Entry
Database: PDB / ID: 5fl6
TitleThree dimensional structure of human carbonic anhydrase IX in complex with 5-(1-(4-Methylphenyl)-1H-1,2,3-triazol-4-yl)thiophene-2- sulfonamide
ComponentsCARBONIC ANHYDRASE IX
KeywordsLYASE / CARBONIC ANHYDRASE IX / CARBONIC ANHYDRASE 9 / CA IX / CA 9
Function / homology
Function and homology information


Regulation of gene expression by Hypoxia-inducible Factor / microvillus membrane / response to testosterone / secretion / molecular function activator activity / Reversible hydration of carbon dioxide / morphogenesis of an epithelium / carbonic anhydrase / carbonate dehydratase activity / basolateral plasma membrane ...Regulation of gene expression by Hypoxia-inducible Factor / microvillus membrane / response to testosterone / secretion / molecular function activator activity / Reversible hydration of carbon dioxide / morphogenesis of an epithelium / carbonic anhydrase / carbonate dehydratase activity / basolateral plasma membrane / response to hypoxia / response to xenobiotic stimulus / nucleolus / zinc ion binding / membrane / plasma membrane
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
ACETIC ACID / Chem-Y0R / Carbonic anhydrase 9
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsLeitans, J. / Tars, K. / Zalubovskis, R.
CitationJournal: J.Med.Chem. / Year: 2015
Title: An Efficient Expression and Crystallization System of the Cancer Asociated Carbonic Anhydrase Isoform Ix.
Authors: Leitans, J. / Kazaks, A. / Balode, A. / Ivanova, J. / Zalubovskis, R. / Supuran, C.T. / Tars, K.
History
DepositionOct 21, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 11, 2015Provider: repository / Type: Initial release
Revision 1.1Dec 9, 2015Group: Database references
Revision 1.2Jan 17, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.3Jan 30, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.method
Revision 1.4Feb 6, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 1.5Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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_database_status.status_code_sf / _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_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.6Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CARBONIC ANHYDRASE IX
B: CARBONIC ANHYDRASE IX
C: CARBONIC ANHYDRASE IX
D: CARBONIC ANHYDRASE IX
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,72218
Polymers112,6914
Non-polymers2,03214
Water20,6271145
1
A: CARBONIC ANHYDRASE IX
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,6514
Polymers28,1731
Non-polymers4783
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: CARBONIC ANHYDRASE IX
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,7115
Polymers28,1731
Non-polymers5384
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: CARBONIC ANHYDRASE IX
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,6514
Polymers28,1731
Non-polymers4783
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: CARBONIC ANHYDRASE IX
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,7115
Polymers28,1731
Non-polymers5384
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)153.220, 153.220, 170.810
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
CARBONIC ANHYDRASE IX / CARBONATE DEHYDRATASE IX / CARBONIC ANHYDRASE IX / CA-IX / CAI X / MEMBRANE ANTIGEN MN / P54/58N / ...CARBONATE DEHYDRATASE IX / CARBONIC ANHYDRASE IX / CA-IX / CAI X / MEMBRANE ANTIGEN MN / P54/58N / RENAL CELL CARCINOMA-ASSOCIATED ANTIGEN G250 / RCC-ASSOCIATED ANTIGEN G250 / PMW1 / CARBONIC ANHYDRASE IX


Mass: 28172.684 Da / Num. of mol.: 4 / Fragment: UNP RESIDUES 137-391 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: KOMAGATAELLA PASTORIS (fungus) / References: UniProt: Q16790, carbonic anhydrase

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Non-polymers , 5 types, 1159 molecules

#2: Chemical
ChemComp-Y0R / 5-[1-(4-methylphenyl)-1,2,3-triazol-4-yl]thiophene-2-sulfonamide


Mass: 320.390 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C13H12N4O2S2
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H4O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1145 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 3.43 Å3/Da / Density % sol: 64.14 % / Description: NONE
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: 1.0 M DI-AMMONIUM HYDROGEN PHOSPHATE, 0.1 M SODIUM ACETATE PH 4.5, PROTEIN 10 MG/ML 5-10 MM INHIBITOR (STOCK SOLUTION WAS 100 MM INHIBITOR DISSOLVED IN 100% DIMETHYL SULFOXIDE) VAPOR ...Details: 1.0 M DI-AMMONIUM HYDROGEN PHOSPHATE, 0.1 M SODIUM ACETATE PH 4.5, PROTEIN 10 MG/ML 5-10 MM INHIBITOR (STOCK SOLUTION WAS 100 MM INHIBITOR DISSOLVED IN 100% DIMETHYL SULFOXIDE) VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I911-3 / Wavelength: 1.1
DetectorType: MARRESEARCH / Detector: CCD / Date: Feb 2, 2015 / Details: MULTILAYER
RadiationMonochromator: SI CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 1.95→48.11 Å / Num. obs: 108977 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 2.9 % / Biso Wilson estimate: 23.6 Å2 / Rmerge(I) obs: 0.15 / Net I/σ(I): 5.2
Reflection shellResolution: 1.95→2.06 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.58 / Mean I/σ(I) obs: 2 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3IAI

3iai


Resolution: 1.95→48 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.939 / SU B: 3.539 / SU ML: 0.097 / Cross valid method: THROUGHOUT / ESU R: 0.122 / ESU R Free: 0.117 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.20004 5344 4.9 %RANDOM
Rwork0.16912 ---
obs0.17067 103629 99.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.692 Å2
Baniso -1Baniso -2Baniso -3
1-0.08 Å20.04 Å20 Å2
2--0.08 Å20 Å2
3----0.26 Å2
Refinement stepCycle: LAST / Resolution: 1.95→48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7710 0 120 1145 8975
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0198064
X-RAY DIFFRACTIONr_bond_other_d0.0020.027477
X-RAY DIFFRACTIONr_angle_refined_deg1.7021.98111020
X-RAY DIFFRACTIONr_angle_other_deg0.907317175
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.89851000
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.03723.09356
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.847151145
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.7261565
X-RAY DIFFRACTIONr_chiral_restr0.0770.21180
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0219185
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021888
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.3462.1924014
X-RAY DIFFRACTIONr_mcbond_other1.3452.1914011
X-RAY DIFFRACTIONr_mcangle_it2.2183.285008
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.912.4274050
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.95→2.001 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.275 399 -
Rwork0.262 7646 -
obs--100 %

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