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- PDB-6sas: Human Carbonic Anhydrase II in complex with fragment. -

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Basic information

Entry
Database: PDB / ID: 6sas
TitleHuman Carbonic Anhydrase II in complex with fragment.
ComponentsCarbonic anhydrase 2
KeywordsLYASE / Inhibitor / Complex / CO2 conversion / fragment
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, 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
Similarity search - Domain/homology
N-[3-(aminomethyl)phenyl]acetamide / (4-CARBOXYPHENYL)(CHLORO)MERCURY / : / Carbonic anhydrase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.1 Å
AuthorsGloeckner, S. / Heine, A. / Klebe, G.
CitationJournal: Biomolecules / Year: 2020
Title: A Proof-of-Concept Fragment Screening of a Hit-Validated 96-Compounds Library against Human Carbonic Anhydrase II.
Authors: Glockner, S. / Heine, A. / Klebe, G.
History
DepositionJul 17, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 15, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: 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 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_comp_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)30,6726
Polymers29,8071
Non-polymers8655
Water3,801211
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area770 Å2
ΔGint-65 kcal/mol
Surface area11330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.383, 41.543, 72.121
Angle α, β, γ (deg.)90.000, 104.334, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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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: 29806.588 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: The first 5 amino acids (GSPEF) are remnants of an expression tag
Source: (gene. exp.) Homo sapiens (human) / Gene: CA2 / Plasmid: pGEX-4T1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Codon plus / References: UniProt: P00918, carbonic anhydrase

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Non-polymers , 6 types, 216 molecules

#2: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-HG / MERCURY (II) ION


Mass: 200.590 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Hg
#5: Chemical ChemComp-BE7 / (4-CARBOXYPHENYL)(CHLORO)MERCURY / P-CHLOROMERCURIBENZOIC ACID


Mass: 357.156 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H5ClHgO2
#6: Chemical ChemComp-463 / N-[3-(aminomethyl)phenyl]acetamide


Mass: 164.204 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H12N2O / Feature type: SUBJECT OF INVESTIGATION
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 211 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.13 Å3/Da / Density % sol: 42.48 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.8
Details: Ammonium sulfate 2.7 M, TRIS 0.1 M, saturated with para-Chloromercuribenzoic acid

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 26, 2016
RadiationMonochromator: Si(111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.097→41.543 Å / Num. obs: 97293 / % possible obs: 97.8 % / Redundancy: 3.64 % / Biso Wilson estimate: 9.02 Å2 / CC1/2: 0.998 / Rsym value: 0.067 / Net I/σ(I): 9.93
Reflection shellResolution: 1.1→1.16 Å / Redundancy: 3.56 % / Num. unique obs: 15236 / CC1/2: 0.789 / Rsym value: 0.458 / % possible all: 95.4

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3KS3

3ks3


Resolution: 1.1→41.06 Å / SU ML: 0.0855 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 13.1598
RfactorNum. reflection% reflection
Rfree0.1486 4865 5 %
Rwork0.1319 --
obs0.1327 97283 97.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 12.38 Å2
Refinement stepCycle: LAST / Resolution: 1.1→41.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2001 0 28 211 2240
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00612398
X-RAY DIFFRACTIONf_angle_d0.93813299
X-RAY DIFFRACTIONf_chiral_restr0.0821343
X-RAY DIFFRACTIONf_plane_restr0.0068452
X-RAY DIFFRACTIONf_dihedral_angle_d12.6622875
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.1-1.110.24441340.22482547X-RAY DIFFRACTION81.84
1.11-1.120.22051640.2063126X-RAY DIFFRACTION98.95
1.12-1.140.19651610.19063047X-RAY DIFFRACTION98.98
1.14-1.150.211640.17333111X-RAY DIFFRACTION99
1.15-1.170.19621630.16373106X-RAY DIFFRACTION98.61
1.17-1.180.21451620.16393074X-RAY DIFFRACTION98.06
1.18-1.20.18571580.15863001X-RAY DIFFRACTION97.53
1.2-1.220.18461580.15693008X-RAY DIFFRACTION94.65
1.22-1.240.17181630.15193092X-RAY DIFFRACTION99.09
1.24-1.260.16321650.13773142X-RAY DIFFRACTION99.76
1.26-1.280.16691630.14273077X-RAY DIFFRACTION99.02
1.28-1.30.15311650.12783138X-RAY DIFFRACTION99.46
1.3-1.330.16511640.12853126X-RAY DIFFRACTION98.98
1.33-1.350.16161620.12823065X-RAY DIFFRACTION98.99
1.35-1.380.17021630.12383096X-RAY DIFFRACTION98.07
1.38-1.410.13091630.11613103X-RAY DIFFRACTION98.46
1.41-1.450.13911600.11623040X-RAY DIFFRACTION97.09
1.45-1.490.13961590.11693014X-RAY DIFFRACTION95.46
1.49-1.530.14461630.10773112X-RAY DIFFRACTION99.45
1.53-1.580.1421640.10743120X-RAY DIFFRACTION99.79
1.58-1.640.12711670.10293166X-RAY DIFFRACTION99.61
1.64-1.70.15581650.11153124X-RAY DIFFRACTION99.43
1.7-1.780.13881640.10883118X-RAY DIFFRACTION99.45
1.78-1.880.13531650.11643140X-RAY DIFFRACTION99.04
1.88-1.990.13061600.11953043X-RAY DIFFRACTION96.42
1.99-2.150.12691610.12233048X-RAY DIFFRACTION96.05
2.15-2.360.14111660.12013164X-RAY DIFFRACTION99.43
2.36-2.710.14251650.12883129X-RAY DIFFRACTION98.65
2.71-3.410.14411650.14173136X-RAY DIFFRACTION98.24
3.41-41.060.13881690.14473205X-RAY DIFFRACTION97.43

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