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- PDB-3mmf: Crystal structure of human carbonic anhydrase II in complex with ... -

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Basic information

Entry
Database: PDB / ID: 3mmf
TitleCrystal 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 / metal-binding / triazine / LYASE / 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 / regulation of chloride transport / arylesterase activity / Reversible hydration of carbon dioxide / positive regulation of synaptic transmission, GABAergic ...positive regulation of cellular pH reduction / positive regulation of dipeptide transmembrane transport / regulation of monoatomic anion transport / secretion / cyanamide hydratase / cyanamide hydratase activity / regulation of chloride transport / arylesterase activity / Reversible hydration of carbon dioxide / positive regulation of synaptic transmission, GABAergic / angiotensin-activated signaling pathway / morphogenesis of an epithelium / 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
Chem-D9H / 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 19, 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
Revision 1.3Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)29,7914
Polymers29,2891
Non-polymers5023
Water5,621312
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)42.336, 41.242, 72.050
Angle α, β, γ (deg.)90.000, 104.310, 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-D9H / 4-({4-chloro-6-[(2-hydroxyethyl)amino]-1,3,5-triazin-2-yl}amino)benzenesulfonamide


Mass: 344.777 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H13ClN6O3S
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: 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 / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.08 Å3/Da / Density % sol: 40.89 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.8
Details: 1.3M sodium citrate, 100Mm tris-hkl., 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 11, 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→24.5 Å / Num. all: 38628 / Num. obs: 38542 / % possible obs: 99.2 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 2 / Redundancy: 3.6 % / Biso Wilson estimate: 29.2 Å2 / Rmerge(I) obs: 0.064 / Χ2: 1.059 / Net I/σ(I): 15.8
Reflection shellResolution: 1.5→1.55 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.341 / Mean I/σ(I) obs: 3.4 / Num. unique all: 3752 / Χ2: 0.947 / % possible all: 97.1

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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→23.836 Å / Occupancy max: 1 / Occupancy min: 0.5 / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.182 1932 5.01 %Random
Rwork0.159 ---
all0.161 38628 --
obs0.16 38542 98.96 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 45.402 Å2 / ksol: 0.451 e/Å3
Displacement parametersBiso max: 89.59 Å2 / Biso mean: 22.195 Å2 / Biso min: 9.41 Å2
Baniso -1Baniso -2Baniso -3
1--1.53 Å20 Å20.979 Å2
2--0.189 Å20 Å2
3---1.341 Å2
Refinement stepCycle: LAST / Resolution: 1.5→23.836 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2049 0 29 312 2390
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012186
X-RAY DIFFRACTIONf_angle_d1.3822979
X-RAY DIFFRACTIONf_chiral_restr0.076307
X-RAY DIFFRACTIONf_plane_restr0.008384
X-RAY DIFFRACTIONf_dihedral_angle_d13.315822
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 (%)
1.499-1.5360.231370.2052505264294
1.536-1.5780.2111310.1772559269098
1.578-1.6250.1841300.1552599272999
1.625-1.6770.1851280.1442592272099
1.677-1.7370.1571420.1272598274099
1.737-1.8060.161270.1232628275599
1.806-1.8880.1461410.12925962737100
1.888-1.9880.1671190.12126272746100
1.988-2.1120.1481470.12326502797100
2.112-2.2760.161370.12626062743100
2.276-2.5040.1641580.13126302788100
2.504-2.8660.1671390.14126522791100
2.866-3.6090.1531460.13426602806100
3.609-23.8380.1591500.1492708285899
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)
10.4307-0.10120.00850.1969-0.00280.4479-0.0031-0.03510.0053-0.03230.00430.00580.01380.0087-0.00350.1196-0.00210.00390.10890.00110.1217-9.6752-1.982615.8517
22.4176-0.3160.12690.1409-0.1010.0792-0.02580.14930.141-0.1126-0.02540.0026-0.097-0.02840.04270.1927-0.01160.00540.1499-0.00520.1579-4.71634.825413.5081
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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