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

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Basic information

Entry
Database: PDB / ID: 6say
TitleHuman Carbonic Anhydrase II in complex with fragment.
ComponentsCarbonic anhydrase 2
KeywordsLYASE / Inhibitor / Complex / CO2 conversion
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 / 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 / cyanamide hydratase activity / arylesterase activity / regulation of chloride transport / Reversible hydration of carbon dioxide / morphogenesis of an epithelium / angiotensin-activated signaling pathway / positive regulation of synaptic transmission, GABAergic / 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 / apical part of cell / myelin sheath / extracellular exosome / zinc ion binding / plasma membrane / cytosol / cytoplasm
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
(4-CARBOXYPHENYL)(CHLORO)MERCURY / : / Chem-L3Q / Carbonic anhydrase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 0.95 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 18, 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)31,0518
Polymers29,8071
Non-polymers1,2457
Water3,963220
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1060 Å2
ΔGint-106 kcal/mol
Surface area11790 Å2
Unit cell
Length a, b, c (Å)42.390, 41.508, 72.214
Angle α, β, γ (deg.)90.000, 104.676, 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, 227 molecules

#2: Chemical ChemComp-ZN / ZINC ION


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


Mass: 200.590 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Hg
#4: Chemical ChemComp-BE7 / (4-CARBOXYPHENYL)(CHLORO)MERCURY / P-CHLOROMERCURIBENZOIC ACID


Mass: 357.156 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H5ClHgO2
#5: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#6: Chemical ChemComp-L3Q / (8~{a}~{S})-1,5,6,7,8,8~{a}-hexahydro-[1,3]oxazolo[3,4-a]pyrazin-3-one


Mass: 142.156 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H10N2O2 / Feature type: SUBJECT OF INVESTIGATION
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 220 / 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: 42.23 %
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: Oct 14, 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: 0.95→41.508 Å / Num. obs: 146380 / % possible obs: 96.5 % / Redundancy: 3.52 % / Biso Wilson estimate: 7.92 Å2 / CC1/2: 0.999 / Rsym value: 0.052 / Net I/σ(I): 11.39
Reflection shellResolution: 0.95→1.01 Å / Redundancy: 2.95 % / Mean I/σ(I) obs: 1.97 / Num. unique obs: 21821 / CC1/2: 0.795 / Rsym value: 0.399 / % possible all: 89.1

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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: 0.95→34.93 Å / SU ML: 0.0786 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 11.1664
RfactorNum. reflection% reflection
Rfree0.1376 7319 5 %
Rwork0.122 --
obs0.1228 146362 96.52 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 11.44 Å2
Refinement stepCycle: LAST / Resolution: 0.95→34.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2071 0 28 220 2319
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00672854
X-RAY DIFFRACTIONf_angle_d0.97343948
X-RAY DIFFRACTIONf_chiral_restr0.0826404
X-RAY DIFFRACTIONf_plane_restr0.0071546
X-RAY DIFFRACTIONf_dihedral_angle_d14.79551070
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
0.95-0.960.24781870.23863557X-RAY DIFFRACTION73.53
0.96-0.970.23932150.21494086X-RAY DIFFRACTION86
0.97-0.990.20912350.19884473X-RAY DIFFRACTION93.01
0.99-10.20032410.18194574X-RAY DIFFRACTION97.12
1-1.010.18272470.17434694X-RAY DIFFRACTION97.42
1.01-1.030.18722420.1654595X-RAY DIFFRACTION97.09
1.03-1.040.19182480.16324706X-RAY DIFFRACTION97.71
1.04-1.060.16392440.14744636X-RAY DIFFRACTION97.6
1.06-1.070.15632450.13564650X-RAY DIFFRACTION97.01
1.07-1.090.12282470.11284708X-RAY DIFFRACTION98.04
1.09-1.110.11842450.10794670X-RAY DIFFRACTION98.28
1.11-1.130.12582480.10354699X-RAY DIFFRACTION98.47
1.13-1.150.13412500.10874747X-RAY DIFFRACTION98.4
1.15-1.170.1182470.10224698X-RAY DIFFRACTION98.47
1.17-1.20.09942440.09284635X-RAY DIFFRACTION98.07
1.2-1.230.11862490.0974733X-RAY DIFFRACTION97.67
1.23-1.260.10822490.09644737X-RAY DIFFRACTION98.56
1.26-1.290.11662500.0954743X-RAY DIFFRACTION98.79
1.29-1.330.10962480.09224710X-RAY DIFFRACTION98.78
1.33-1.370.11222500.09634760X-RAY DIFFRACTION98.99
1.37-1.420.11552500.09894733X-RAY DIFFRACTION98.73
1.42-1.480.11382450.09764668X-RAY DIFFRACTION96.77
1.48-1.550.11762490.09914725X-RAY DIFFRACTION98.77
1.55-1.630.10882490.10324731X-RAY DIFFRACTION98.5
1.63-1.730.11632490.10424737X-RAY DIFFRACTION98.29
1.73-1.860.12552490.11014726X-RAY DIFFRACTION98.18
1.86-2.050.12612420.1184606X-RAY DIFFRACTION95.06
2.05-2.350.12812500.12024750X-RAY DIFFRACTION98.17
2.35-2.960.16262520.14274774X-RAY DIFFRACTION97.69
2.96-34.930.16172510.14144784X-RAY DIFFRACTION96.55

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