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- PDB-5eh7: human carbonic anhydrase II in complex with ligand -

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Basic information

Entry
Database: PDB / ID: 5eh7
Titlehuman carbonic anhydrase II in complex with ligand
ComponentsCarbonic anhydrase 2
KeywordsLYASE / human carbonic anhydrase
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 activity / cyanamide hydratase / 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 activity / cyanamide hydratase / arylesterase activity / regulation of chloride transport / Reversible hydration of carbon dioxide / morphogenesis of an epithelium / angiotensin-activated signaling pathway / regulation of intracellular pH / positive regulation of synaptic transmission, GABAergic / 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 / apical part of cell / myelin sheath / extracellular exosome / zinc ion binding / plasma membrane / cytoplasm / cytosol
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-5O5 / FORMIC ACID / Carbonic anhydrase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.425 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 28, 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_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.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _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 / _pdbx_struct_oper_list.symmetry_operation / _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_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)29,6695
Polymers29,2891
Non-polymers3794
Water7,404411
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area260 Å2
ΔGint-7 kcal/mol
Surface area11450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.317, 41.601, 72.032
Angle α, β, γ (deg.)90.00, 104.06, 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 , 5 types, 415 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH2O2
#4: Chemical ChemComp-5O5 / 5-[[3,4-bis(chloranyl)phenoxy]methyl]-1~{H}-1,2,3,4-tetrazole


Mass: 245.065 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H6Cl2N4O
#5: Chemical ChemComp-NA / SODIUM ION


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


Mass: 18.015 Da / Num. of mol.: 411 / 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: 2.1 Å3/Da / Density % sol: 41.43 %
Crystal growTemperature: 280 K / Method: vapor diffusion, sitting drop / Details: ammonium sulfate, tris chloride / PH range: 8.61

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.99 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 8, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99 Å / Relative weight: 1
ReflectionResolution: 1.425→41.6 Å / Num. obs: 45538 / % possible obs: 99.7 % / Redundancy: 7.3 % / Net I/σ(I): 12.9

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementResolution: 1.425→39.877 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 17.02 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1743 2007 4.41 %
Rwork0.1454 --
obs0.1467 45518 99.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.425→39.877 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2039 0 20 411 2470
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0142252
X-RAY DIFFRACTIONf_angle_d1.4683077
X-RAY DIFFRACTIONf_dihedral_angle_d14.189848
X-RAY DIFFRACTIONf_chiral_restr0.078317
X-RAY DIFFRACTIONf_plane_restr0.009407
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4253-1.4610.27481560.21872991X-RAY DIFFRACTION97
1.461-1.50050.21981220.19733094X-RAY DIFFRACTION100
1.5005-1.54460.25821460.1893073X-RAY DIFFRACTION100
1.5446-1.59450.19211470.17153115X-RAY DIFFRACTION100
1.5945-1.65150.20421330.16863094X-RAY DIFFRACTION100
1.6515-1.71760.20691590.16013077X-RAY DIFFRACTION100
1.7176-1.79580.21441280.15523148X-RAY DIFFRACTION100
1.7958-1.89040.1881470.14563089X-RAY DIFFRACTION100
1.8904-2.00890.16991430.13483100X-RAY DIFFRACTION100
2.0089-2.1640.14371420.12923117X-RAY DIFFRACTION100
2.164-2.38170.16941430.13223115X-RAY DIFFRACTION100
2.3817-2.72630.17721450.14083129X-RAY DIFFRACTION100
2.7263-3.43460.1551400.13373157X-RAY DIFFRACTION100
3.4346-39.89260.1411560.13393212X-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)
12.72010.3818-0.85491.1864-0.25651.644-0.0455-0.0167-0.0413-0.05340.0054-0.21470.0410.20970.03780.0560.01090.00140.0935-0.00450.092726.0289-2.466820.6913
20.9837-1.14321.02821.8015-1.55313.7589-0.3582-0.44140.0230.28020.43510.0698-0.1228-0.5879-0.06850.1250.03150.02460.22860.00930.13051.6876-0.618832.5068
31.0796-0.2946-0.19840.9536-0.00061.3760.02370.08790.0977-0.07960.00430.0832-0.0967-0.0818-0.02750.0661-0.0121-0.00840.06980.00910.09158.04761.184713.8864
40.76150.67960.09272.61790.70541.15760.01460.00080.0666-0.0286-0.02010.135-0.0383-0.02860.01320.05920.0044-0.00350.06020.00220.06579.2743.534517.8735
56.05173.2229-2.36933.539-2.06794.2079-0.22830.6965-0.1147-0.40550.25090.1920.2994-0.4162-0.00760.138-0.0233-0.03060.1564-0.02230.11155.4559-6.26890.1541
61.05870.02860.00860.4280.12881.04820.00190.09510.003-0.06470.01590.0445-0.008-0.0731-0.0160.06220.0012-0.00630.05410.00660.06748.3164-0.951414.7207
72.05170.0008-0.99971.8376-0.86652.4817-0.06290.3509-0.2379-0.2557-0.0231-0.12910.20970.14460.10980.14450.01090.00580.1597-0.03170.075916.0694-10.52421.1241
81.4939-0.3380.53721.23570.86871.35810.0048-0.1879-0.04830.03150.0804-0.05120.03960.0813-0.08470.0614-0.00570.00420.03630.02340.060415.9473-5.965123.9029
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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