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- PDB-6g3v: Crystal structure of human carbonic anhydrase I in complex with t... -

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Basic information

Entry
Database: PDB / ID: 6g3v
TitleCrystal structure of human carbonic anhydrase I in complex with the inhibitor famotidine
ComponentsCarbonic anhydrase 1
KeywordsLYASE
Function / homology
Function and homology information


hydro-lyase activity / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / cyanamide hydratase / cyanamide hydratase activity / arylesterase activity / Reversible hydration of carbon dioxide / carbonic anhydrase / carbonate dehydratase activity / Erythrocytes take up oxygen and release carbon dioxide / Erythrocytes take up carbon dioxide and release oxygen ...hydro-lyase activity / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / cyanamide hydratase / cyanamide hydratase activity / arylesterase activity / Reversible hydration of carbon dioxide / carbonic anhydrase / carbonate dehydratase activity / Erythrocytes take up oxygen and release carbon dioxide / Erythrocytes take up carbon dioxide and release oxygen / one-carbon metabolic process / extracellular exosome / zinc ion binding / cytosol
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
famotidine / Carbonic anhydrase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.69 Å
AuthorsFerraroni, M. / Supuran, C.T. / Angeli, A.
CitationJournal: ACS Med Chem Lett / Year: 2018
Title: Famotidine, an Antiulcer Agent, Strongly InhibitsHelicobacter pyloriand Human Carbonic Anhydrases.
Authors: Angeli, A. / Ferraroni, M. / Supuran, C.T.
History
DepositionMar 26, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 28, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 17, 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.ptnr1_auth_asym_id / _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_asym_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Carbonic anhydrase 1
B: Carbonic anhydrase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,8989
Polymers57,8122
Non-polymers1,0867
Water2,864159
1
A: Carbonic anhydrase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,3113
Polymers28,9061
Non-polymers4052
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Carbonic anhydrase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,5876
Polymers28,9061
Non-polymers6815
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)62.507, 71.369, 121.442
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Carbonic anhydrase 1 / Carbonate dehydratase I / Carbonic anhydrase B / CAB / Carbonic anhydrase I / CA-I


Mass: 28906.186 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: erytrocytes / Source: (natural) Homo sapiens (human) / References: UniProt: P00915, carbonic anhydrase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-FO9 / famotidine


Mass: 339.461 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H17N7O2S3 / Comment: medication, antagonist*YM
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 159 / 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: 2.34 Å3/Da / Density % sol: 47.5 %
Crystal growTemperature: 296 K / Method: vapor diffusion / pH: 9 / Details: 28% PEG4000, 0.2 M sodium acetate, Tris 100 mM

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.873 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Jan 27, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.873 Å / Relative weight: 1
ReflectionResolution: 1.69→30 Å / Num. all: 158183 / Num. obs: 57352 / % possible obs: 93.5 % / Redundancy: 2.75 % / CC1/2: 0.99 / Rrim(I) all: 0.083 / Rsym value: 0.068 / Net I/σ(I): 8.3
Reflection shellResolution: 1.69→1.8 Å / Redundancy: 2.2 % / Num. unique obs: 8041 / CC1/2: 0.37 / Rrim(I) all: 0.151 / Rsym value: 0.12 / % possible all: 82.6

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Processing

Software
NameVersionClassification
REFMACrefinement
PDB_EXTRACT3.24data extraction
XDSdata reduction
XSCALEdata scaling
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 3LXE

3lxe


Resolution: 1.69→27 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.942 / SU B: 4.37 / SU ML: 0.128 / SU R Cruickshank DPI: 0.1275 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.128 / ESU R Free: 0.13 / Details: U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2631 2927 5.1 %RANDOM
Rwork0.2142 ---
obs0.2167 54371 93.57 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 114.34 Å2 / Biso mean: 30.799 Å2 / Biso min: 14.93 Å2
Baniso -1Baniso -2Baniso -3
1--1.05 Å2-0 Å20 Å2
2--2.15 Å2-0 Å2
3----1.1 Å2
Refinement stepCycle: final / Resolution: 1.69→27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4001 0 80 159 4240
Biso mean--57.28 31.42 -
Num. residues----513
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.0194220
X-RAY DIFFRACTIONr_angle_refined_deg2.1991.9355745
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4155523
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.20624.709189
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.71115655
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.5271514
X-RAY DIFFRACTIONr_chiral_restr0.1530.2611
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0213324
LS refinement shellResolution: 1.693→1.737 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.468 165 -
Rwork0.455 3051 -
all-3216 -
obs--72.22 %

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