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- PDB-3mna: The crystal structure of human carbonic anhydrase Ii in complex w... -

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Basic information

Entry
Database: PDB / ID: 3mna
TitleThe crystal structure of human carbonic anhydrase Ii in complex with a 1,3,5-triazine-substituted benzenesulfonamide inhibitor
ComponentsCarbonic anhydrase 2
Keywordslyase/lyase inhibitor / zinc metalloenzyme / inhibitor / sulfonamide / lyase / triazine / lyase-lyase inhibitor complex
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 / angiotensin-activated signaling pathway / Reversible hydration of carbon dioxide ...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 / angiotensin-activated signaling pathway / Reversible hydration of carbon dioxide / regulation of intracellular pH / positive regulation of synaptic transmission, GABAergic / hydro-lyase activity / 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 / apical part of cell / one-carbon metabolic process / 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-DWH / Carbonic anhydrase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsAvvaru, B.S. / Wagner, J. / Robbins, A.H. / Mckenna, R.
CitationJournal: Bioorg.Med.Chem. / Year: 2011
Title: Sulfonamides incorporating 1,3,5-triazine moieties selectively and potently inhibit carbonic anhydrase transmembrane isoforms IX, XII and XIV over cytosolic isoforms I and II: Solution and X- ...Title: Sulfonamides incorporating 1,3,5-triazine moieties selectively and potently inhibit carbonic anhydrase transmembrane isoforms IX, XII and XIV over cytosolic isoforms I and II: Solution and X-ray crystallographic studies.
Authors: Carta, F. / Garaj, V. / Maresca, A. / Wagner, J. / Avvaru, B.S. / Robbins, A.H. / Scozzafava, A. / McKenna, R. / Supuran, C.T.
History
DepositionApr 21, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 20, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Carbonic anhydrase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,8194
Polymers29,2891
Non-polymers5303
Water6,125340
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)42.360, 41.230, 72.023
Angle α, β, γ (deg.)90.000, 104.240, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#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, HCA2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)PLYSS / References: UniProt: P00918, carbonic anhydrase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-DWH / methyl N-{4-chloro-6-[(4-sulfamoylphenyl)amino]-1,3,5-triazin-2-yl}glycinate


Mass: 372.787 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H13ClN6O4S
#4: 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
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 340 / 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: 2.08 Å3/Da / Density % sol: 40.9 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.8
Details: 1.3M sodium citrate, 100mM tris-hcl, pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Mar 12, 2010 / Details: mirrors
RadiationMonochromator: Rigaku Varimax / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.5→25.3 Å / Num. all: 38812 / Num. obs: 38719 / % possible obs: 99.7 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 2 / Redundancy: 4 % / Biso Wilson estimate: 23.8 Å2 / Rmerge(I) obs: 0.071 / Χ2: 1.055 / Net I/σ(I): 15
Reflection shellResolution: 1.5→1.55 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.316 / Mean I/σ(I) obs: 4.5 / Num. unique all: 3826 / Χ2: 1.043 / % possible all: 99

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIX1.6.1_348refinement
PDB_EXTRACT3.1data extraction
CrystalCleardata collection
PHENIX1.6.1_348phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2ILI

2ili


Resolution: 1.5→25.3 Å / Occupancy max: 1 / Occupancy min: 0.2 / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 0.16 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.169 1941 5.01 %Random
Rwork0.145 ---
obs0.147 38719 99.44 %-
all-38812 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 44.353 Å2 / ksol: 0.448 e/Å3
Displacement parametersBiso max: 87.13 Å2 / Biso mean: 18.658 Å2 / Biso min: 6.56 Å2
Baniso -1Baniso -2Baniso -3
1--0.085 Å20 Å21.058 Å2
2---1.56 Å20 Å2
3---1.645 Å2
Refinement stepCycle: LAST / Resolution: 1.5→25.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2049 0 31 340 2420
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092179
X-RAY DIFFRACTIONf_angle_d1.3442968
X-RAY DIFFRACTIONf_chiral_restr0.078306
X-RAY DIFFRACTIONf_plane_restr0.006385
X-RAY DIFFRACTIONf_dihedral_angle_d14.242814
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.499-1.5370.221330.1892585271897
1.537-1.5780.1941450.17125782723100
1.578-1.6250.1891270.15226382765100
1.625-1.6770.1971350.1462598273399
1.677-1.7370.1641390.1362616275599
1.737-1.8060.1571490.1252614276399
1.806-1.8890.1481450.12625922737100
1.889-1.9880.1531160.11526362752100
1.988-2.1130.1391440.1152645278999
2.113-2.2760.1431250.12126222747100
2.276-2.5050.151440.12726402784100
2.505-2.8670.1581540.13326282782100
2.867-3.610.1511350.13126722807100
3.61-25.3350.1621500.1462714286499
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)
10.4201-0.09470.03660.2549-0.01280.5166-0.0059-0.0390.0093-0.02150.00580.00530.00880.0009-0.00120.0712-0.00260.00670.06530.00080.0871-9.6525-1.391915.9349
20.42280.1597-0.33170.0742-0.13230.2640.02710.01610.0755-0.01640.00420.0997-0.01160.053-0.03070.1029-0.01350.0170.10410.00480.1259-4.33345.571613.0615
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain A and not element HA0
2X-RAY DIFFRACTION2chain I and not element HA - I0

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