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- PDB-6sdj: Human Carbonic Anhydrase II in complex with (R)-1-aminopropan-2-ol -

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Basic information

Entry
Database: PDB / ID: 6sdj
TitleHuman Carbonic Anhydrase II in complex with (R)-1-aminopropan-2-ol
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 / : / (2~{R})-1-azanylpropan-2-ol / Carbonic anhydrase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.02 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 27, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 15, 2020Provider: repository / Type: Initial release
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_label_atom_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _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
Revision 2.1Jan 24, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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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)31,0637
Polymers29,8071
Non-polymers1,2566
Water3,225179
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area950 Å2
ΔGint-52 kcal/mol
Surface area11140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.359, 41.103, 72.174
Angle α, β, γ (deg.)90.000, 104.187, 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
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 , 5 types, 185 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-J3K / (2~{R})-1-azanylpropan-2-ol


Mass: 75.110 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H9NO / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-HG / MERCURY (II) ION


Mass: 200.590 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Hg
#5: Chemical ChemComp-BE7 / (4-CARBOXYPHENYL)(CHLORO)MERCURY / P-CHLOROMERCURIBENZOIC ACID


Mass: 357.156 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H5ClHgO2 / Comment: protease inhibitor*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 179 / 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: 2.05 Å3/Da / Density % sol: 39.9 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: Ammonium sulfate 2.7 M, TRIS 0.1, 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: 14.2 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS3 S 2M / Detector: PIXEL / Date: Mar 10, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.02→41.103 Å / Num. obs: 120252 / % possible obs: 98.1 % / Redundancy: 3.5 % / Biso Wilson estimate: 9.64 Å2 / CC1/2: 0.998 / Rsym value: 0.048 / Net I/σ(I): 13.51
Reflection shellResolution: 1.02→1.08 Å / Mean I/σ(I) obs: 3.74 / Num. unique obs: 18157 / CC1/2: 0.96 / Rsym value: 0.175 / % possible all: 92.1

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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: 1.02→35.44 Å / SU ML: 0.0518 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 10.537
RfactorNum. reflection% reflectionSelection details
Rfree0.1396 6013 5 %Random selection of 5 %
Rwork0.1283 ---
obs0.1289 120242 98.1 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 13.52 Å2
Refinement stepCycle: LAST / Resolution: 1.02→35.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2011 0 28 179 2218
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00622486
X-RAY DIFFRACTIONf_angle_d1.01013416
X-RAY DIFFRACTIONf_chiral_restr0.0807354
X-RAY DIFFRACTIONf_plane_restr0.0074460
X-RAY DIFFRACTIONf_dihedral_angle_d14.8009909
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.02-1.030.17861540.15742917X-RAY DIFFRACTION75.42
1.03-1.040.15011760.14633353X-RAY DIFFRACTION87.63
1.04-1.060.13872020.1363832X-RAY DIFFRACTION98.99
1.06-1.070.14932010.12573811X-RAY DIFFRACTION99.68
1.07-1.080.12692050.11443906X-RAY DIFFRACTION99.78
1.08-1.10.12092020.11323829X-RAY DIFFRACTION99.85
1.1-1.110.13162050.1123910X-RAY DIFFRACTION99.85
1.11-1.130.11752010.10723806X-RAY DIFFRACTION99.9
1.13-1.150.12932030.10563859X-RAY DIFFRACTION99.8
1.15-1.170.11942030.10593851X-RAY DIFFRACTION99.68
1.17-1.190.11792030.1043858X-RAY DIFFRACTION99.85
1.19-1.210.12812040.10673890X-RAY DIFFRACTION99.76
1.21-1.230.12552020.10463834X-RAY DIFFRACTION99.63
1.23-1.260.13312030.10463858X-RAY DIFFRACTION99.8
1.26-1.280.11252060.1023910X-RAY DIFFRACTION99.69
1.28-1.310.10482000.10023797X-RAY DIFFRACTION99.3
1.31-1.350.1072020.10283849X-RAY DIFFRACTION99.53
1.35-1.380.12052030.10663847X-RAY DIFFRACTION99.24
1.38-1.420.12122020.1043837X-RAY DIFFRACTION99.12
1.42-1.470.11272020.10373840X-RAY DIFFRACTION98.8
1.47-1.520.11212020.10273841X-RAY DIFFRACTION99.04
1.52-1.580.12492010.10613815X-RAY DIFFRACTION98.65
1.58-1.660.11652030.10773849X-RAY DIFFRACTION98.81
1.66-1.740.11572010.11113822X-RAY DIFFRACTION98.48
1.74-1.850.12922040.11513882X-RAY DIFFRACTION98.81
1.85-20.14632000.11873790X-RAY DIFFRACTION98.2
2-2.20.13332030.12883864X-RAY DIFFRACTION98.43
2.2-2.510.13652030.1393856X-RAY DIFFRACTION98.64
2.51-3.170.16832050.15793905X-RAY DIFFRACTION98.87
3.17-35.440.17372120.1614011X-RAY DIFFRACTION99.6

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