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

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Basic information

Entry
Database: PDB / ID: 5ehv
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 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-5ON / FORMIC ACID / Carbonic anhydrase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.208 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_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _pdbx_struct_oper_list.symmetry_operation / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_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)29,8286
Polymers29,2891
Non-polymers5395
Water6,882382
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area480 Å2
ΔGint-6 kcal/mol
Surface area11820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.139, 41.332, 72.106
Angle α, β, γ (deg.)90.00, 104.25, 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, 387 molecules

#2: Chemical ChemComp-5ON / (~{E})-3-[3-[[3-(2-hydroxy-2-oxoethyl)phenyl]methoxy]phenyl]prop-2-enoic acid


Mass: 312.317 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H16O5
#3: Chemical ChemComp-ZN / ZINC ION


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


Mass: 46.025 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH2O2
#5: 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
#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.: 382 / 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: 2.08 Å3/Da / Density % sol: 40.81 %
Crystal growTemperature: 280 K / Method: vapor diffusion, sitting drop / Details: ammonium sulfate, tris-chloride / PH range: 8.36

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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: 1.208→41.3 Å / Num. obs: 70578 / % possible obs: 95.9 % / Redundancy: 6.9 % / Net I/σ(I): 10.9

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementResolution: 1.208→39.787 Å / SU ML: 0.08 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 16.35 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1746 1987 2.82 %
Rwork0.1532 --
obs0.1538 70559 95.61 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.208→39.787 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2059 0 34 382 2475
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0132269
X-RAY DIFFRACTIONf_angle_d1.4583093
X-RAY DIFFRACTIONf_dihedral_angle_d14.498855
X-RAY DIFFRACTIONf_chiral_restr0.07317
X-RAY DIFFRACTIONf_plane_restr0.009408
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.2085-1.23870.24141260.20464595X-RAY DIFFRACTION90
1.2387-1.27220.21871460.19554749X-RAY DIFFRACTION94
1.2722-1.30960.16991300.17524802X-RAY DIFFRACTION94
1.3096-1.35190.21231440.17234799X-RAY DIFFRACTION94
1.3519-1.40020.20541350.16854854X-RAY DIFFRACTION95
1.4002-1.45630.17731340.1594870X-RAY DIFFRACTION95
1.4563-1.52260.17811520.15684856X-RAY DIFFRACTION96
1.5226-1.60280.1671440.15014913X-RAY DIFFRACTION96
1.6028-1.70330.15561400.14674918X-RAY DIFFRACTION96
1.7033-1.83480.16931510.14344958X-RAY DIFFRACTION97
1.8348-2.01940.15431460.14225025X-RAY DIFFRACTION98
2.0194-2.31160.16371460.14525037X-RAY DIFFRACTION98
2.3116-2.91220.15171440.15355092X-RAY DIFFRACTION98
2.9122-39.80810.18751490.14735104X-RAY DIFFRACTION97
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)
11.63910.5426-1.03730.4093-0.65781.6588-0.0751-0.0115-0.0493-0.0162-0.0243-0.34710.01280.20060.06980.04670.00540.02240.122-0.00340.168227.9915-1.210318.5573
21.414-0.74120.24191.5967-0.30011.9155-0.0634-0.07950.1216-0.04850.10390.1427-0.1978-0.2631-0.06630.0793-0.0135-0.02020.0788-0.00270.10515.70092.962917.6021
31.2081-0.3819-0.26211.90340.14491.462-0.0166-0.04350.0184-0.05780.02960.0893-0.0114-0.0066-0.0050.0304-0.0152-0.00280.05130.00170.05189.4558-3.257218.5725
41.00640.44330.12662.87360.70861.38530.0031-0.02580.0761-0.1066-0.00250.0947-0.0873-0.00290.00640.04730.00730.00110.05680.00530.04569.1343.525817.8461
50.91490.0744-0.02791.10610.22510.9932-0.02880.1439-0.0221-0.25560.03080.0449-0.0009-0.04290.01070.097-0.0041-0.00980.06440.01040.05639.606-3.93829.2965
61.7526-0.25790.29941.7570.98091.6528-0.0318-0.2233-0.00580.06020.1262-0.06260.00550.1267-0.10230.04590.00390.00450.04040.02930.053715.6198-5.873923.9377
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 29 )
2X-RAY DIFFRACTION2chain 'A' and (resid 30 through 77 )
3X-RAY DIFFRACTION3chain 'A' and (resid 78 through 115 )
4X-RAY DIFFRACTION4chain 'A' and (resid 116 through 153 )
5X-RAY DIFFRACTION5chain 'A' and (resid 154 through 237 )
6X-RAY DIFFRACTION6chain 'A' and (resid 238 through 260 )

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