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

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Basic information

Entry
Database: PDB / ID: 6rmp
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 dipeptide transmembrane transport / positive regulation of cellular pH reduction / Developmental Lineage of Pancreatic Ductal Cells / regulation of monoatomic anion transport / secretion / cyanamide hydratase / cyanamide hydratase activity / arylesterase activity / regulation of chloride transport / Reversible hydration of carbon dioxide ...positive regulation of dipeptide transmembrane transport / positive regulation of cellular pH reduction / Developmental Lineage of Pancreatic Ductal Cells / 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 / 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
3-(dimethylamino)benzohydrazide / (4-CARBOXYPHENYL)(CHLORO)MERCURY / Carbonic anhydrase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.22 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
DepositionMay 7, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 15, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)30,4875
Polymers29,8071
Non-polymers6804
Water3,729207
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area470 Å2
ΔGint1 kcal/mol
Surface area11360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.405, 41.547, 72.075
Angle α, β, γ (deg.)90.00, 104.65, 90.00
Int Tables number4
Space group name H-MP1211

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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 , 5 types, 211 molecules

#2: Chemical ChemComp-BE7 / (4-CARBOXYPHENYL)(CHLORO)MERCURY / P-CHLOROMERCURIBENZOIC ACID


Mass: 357.156 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H5ClHgO2 / Comment: protease inhibitor*YM
#3: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#4: Chemical ChemComp-47S / 3-(dimethylamino)benzohydrazide


Mass: 179.219 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H13N3O / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 207 / 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: 2.2 Å3/Da / Density % sol: 44.11 %
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: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.7999 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 6, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.7999 Å / Relative weight: 1
ReflectionResolution: 1.22→41.547 Å / Num. obs: 72050 / % possible obs: 98.6 % / Redundancy: 3.72 % / Biso Wilson estimate: 9.9 Å2 / CC1/2: 0.998 / Rsym value: 0.068 / Net I/σ(I): 10.17
Reflection shellResolution: 1.22→1.29 Å / Redundancy: 3.72 % / Mean I/σ(I) obs: 2.36 / Num. unique obs: 11150 / CC1/2: 0.853 / Rsym value: 0.433 / % possible all: 94.8

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3KS3

3ks3


Resolution: 1.22→34.865 Å / SU ML: 0.09 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 13.89
RfactorNum. reflection% reflectionSelection details
Rfree0.162 3602 5 %Random selection of 5 %
Rwork0.1315 ---
obs0.133 72043 98.61 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.22→34.865 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2017 0 27 207 2251
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072307
X-RAY DIFFRACTIONf_angle_d0.9893174
X-RAY DIFFRACTIONf_dihedral_angle_d12.367845
X-RAY DIFFRACTIONf_chiral_restr0.083326
X-RAY DIFFRACTIONf_plane_restr0.007441
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.2164-1.23240.20661130.18992151X-RAY DIFFRACTION81
1.2324-1.24930.16991380.18322624X-RAY DIFFRACTION99
1.2493-1.26710.20461400.17122648X-RAY DIFFRACTION100
1.2671-1.28610.2111370.16972608X-RAY DIFFRACTION99
1.2861-1.30610.2151380.16812615X-RAY DIFFRACTION100
1.3061-1.32760.19091390.16212645X-RAY DIFFRACTION99
1.3276-1.35050.18631390.1552648X-RAY DIFFRACTION99
1.3505-1.3750.17391380.13832622X-RAY DIFFRACTION99
1.375-1.40150.16971390.13712642X-RAY DIFFRACTION100
1.4015-1.43010.15731410.13722666X-RAY DIFFRACTION100
1.4301-1.46120.15871400.12962658X-RAY DIFFRACTION100
1.4612-1.49520.151370.1232605X-RAY DIFFRACTION100
1.4952-1.53250.15111400.12012671X-RAY DIFFRACTION99
1.5325-1.5740.15471400.11842657X-RAY DIFFRACTION99
1.574-1.62030.14711380.11412610X-RAY DIFFRACTION99
1.6203-1.67260.15891390.11232641X-RAY DIFFRACTION99
1.6726-1.73240.14851410.11182682X-RAY DIFFRACTION100
1.7324-1.80170.13521400.11442667X-RAY DIFFRACTION100
1.8017-1.88370.13481390.11062643X-RAY DIFFRACTION99
1.8837-1.9830.14091410.11682667X-RAY DIFFRACTION100
1.983-2.10730.15341390.11352658X-RAY DIFFRACTION99
2.1073-2.26990.13871400.11592658X-RAY DIFFRACTION100
2.2699-2.49830.14651420.12292688X-RAY DIFFRACTION100
2.4983-2.85970.15031390.13432650X-RAY DIFFRACTION99
2.8597-3.60230.16741410.14382677X-RAY DIFFRACTION99
3.6023-34.87970.1941450.14262739X-RAY DIFFRACTION98

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