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- PDB-5ehw: human carbonic anhydrase II in complex with ligand -

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Basic information

Entry
Database: PDB / ID: 5ehw
Titlehuman carbonic anhydrase II in complex with ligand
ComponentsCarbonic anhydrase 2
KeywordsTRANSFERASE / human carbonic anhydrase II
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 / morphogenesis of an epithelium ...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 / morphogenesis of an epithelium / angiotensin-activated signaling pathway / positive regulation of synaptic transmission, GABAergic / regulation of intracellular pH / 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
(~{E})-3-(2,4-dichlorophenyl)prop-2-enoic acid / FORMIC ACID / Carbonic anhydrase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.392 Å
AuthorsRen, B.
CitationJournal: J.Med.Chem. / Year: 2016
Title: Native State Mass Spectrometry, Surface Plasmon Resonance, and X-ray Crystallography Correlate Strongly as a Fragment Screening Combination.
Authors: Woods, L.A. / Dolezal, O. / Ren, B. / Ryan, J.H. / Peat, T.S. / Poulsen, S.A.
History
DepositionOct 29, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 9, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 23, 2016Group: Database references
Revision 1.2Mar 6, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / diffrn_source / pdbx_struct_conn_angle / pdbx_struct_oper_list / struct_conn
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _pdbx_struct_oper_list.symmetry_operation / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_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_conn.ptnr2_symmetry

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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)29,7336
Polymers29,2891
Non-polymers4445
Water5,621312
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area540 Å2
ΔGint-11 kcal/mol
Surface area11790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.280, 41.699, 72.344
Angle α, β, γ (deg.)90.00, 103.95, 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 / 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) / References: UniProt: P00918, carbonic anhydrase

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Non-polymers , 6 types, 317 molecules

#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C3H8O3
#3: Chemical ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH2O2
#4: Chemical ChemComp-5OO / (~{E})-3-(2,4-dichlorophenyl)prop-2-enoic acid


Mass: 217.049 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H6Cl2O2
#5: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#6: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 312 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.11 Å3/Da / Density % sol: 41.79 %
Crystal growTemperature: 280 K / Method: vapor diffusion, sitting drop / Details: ammonium sulfate, tris-chloride / PH range: 8.32

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.99 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 9, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99 Å / Relative weight: 1
ReflectionResolution: 1.392→41.7 Å / Num. obs: 49135 / % possible obs: 99.7 % / Redundancy: 6.1 % / Net I/σ(I): 11.3

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementResolution: 1.392→39.86 Å / SU ML: 0.11 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 15.44 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1685 2004 4.08 %
Rwork0.1514 --
obs0.1521 49119 99.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.392→39.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2059 0 24 312 2395
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082267
X-RAY DIFFRACTIONf_angle_d1.2013093
X-RAY DIFFRACTIONf_dihedral_angle_d14.48850
X-RAY DIFFRACTIONf_chiral_restr0.053318
X-RAY DIFFRACTIONf_plane_restr0.006409
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3922-1.4270.25321430.2433224X-RAY DIFFRACTION98
1.427-1.46560.22461350.20643376X-RAY DIFFRACTION100
1.4656-1.50870.22821430.18743353X-RAY DIFFRACTION100
1.5087-1.55740.18161530.17583340X-RAY DIFFRACTION100
1.5574-1.61310.18871320.16173356X-RAY DIFFRACTION100
1.6131-1.67770.18291470.15563367X-RAY DIFFRACTION100
1.6777-1.7540.19721440.14643353X-RAY DIFFRACTION100
1.754-1.84650.15671330.13783364X-RAY DIFFRACTION100
1.8465-1.96220.15191430.13513359X-RAY DIFFRACTION100
1.9622-2.11370.15631510.13583376X-RAY DIFFRACTION100
2.1137-2.32640.17861370.1383378X-RAY DIFFRACTION100
2.3264-2.6630.15951520.14843386X-RAY DIFFRACTION100
2.663-3.35480.13691450.14553393X-RAY DIFFRACTION100
3.3548-39.87610.16261460.14663490X-RAY DIFFRACTION100
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)
12.58140.5165-0.70211.1765-0.43081.5475-0.0326-0.0639-0.02460.0291-0.0137-0.20070.0540.23540.01570.04920.0086-0.01010.0826-0.00480.074825.6366-2.519221.0912
20.3275-0.6720.561.5731-1.39352.9851-0.3501-0.4984-0.01460.3010.67140.2415-0.1337-0.6976-0.17080.15680.07040.02860.31810.04410.1341.6402-0.943732.6408
31.396-0.1918-0.61281.01460.1521.31930.06470.14810.1649-0.0890.00750.0687-0.1181-0.1273-0.03480.0659-0.0021-0.010.06290.0230.0748.05881.236214.0347
41.09180.4179-0.28692.0720.24251.56890.05670.01370.13990.0394-0.03030.1208-0.0203-0.0311-0.00180.04360.0074-0.00550.04050.00760.05339.28083.540918.0208
55.98073.202-1.99123.3386-1.26021.8536-0.19230.6571-0.0365-0.45960.24560.13650.221-0.512-0.02030.1624-0.0398-0.04840.2161-0.00180.09385.3833-5.78540.147
61.1009-0.0862-0.43350.71240.04161.06670.03150.14410.0661-0.06920.01380.05750.0157-0.1151-0.02520.05570.002-0.01540.05940.01540.04558.1623-0.868915.0907
71.3404-0.1779-0.15992.0462-0.50311.91-0.09270.3275-0.2274-0.381-0.0448-0.20630.18540.03940.140.1673-0.00650.02050.1447-0.01530.075915.7673-10.49191.0765
81.5971-0.12310.22011.23080.66531.6782-0.0161-0.2141-0.01310.07270.0722-0.05890.00490.1949-0.07280.0654-0.0015-0.00840.02220.0230.052715.6558-6.044723.9434
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 5 through 34 )
2X-RAY DIFFRACTION2chain 'A' and (resid 35 through 50 )
3X-RAY DIFFRACTION3chain 'A' and (resid 51 through 115 )
4X-RAY DIFFRACTION4chain 'A' and (resid 116 through 153 )
5X-RAY DIFFRACTION5chain 'A' and (resid 154 through 166 )
6X-RAY DIFFRACTION6chain 'A' and (resid 167 through 218 )
7X-RAY DIFFRACTION7chain 'A' and (resid 219 through 237 )
8X-RAY DIFFRACTION8chain 'A' and (resid 238 through 260 )

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