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- PDB-4gqr: Human Pancreatic alpha-amylase in complex with myricetin -

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Basic information

Entry
Database: PDB / ID: 4gqr
TitleHuman Pancreatic alpha-amylase in complex with myricetin
ComponentsPancreatic alpha-amylase
KeywordsHYDROLASE/HYDROLASE INHIBITOR / glycosyl hydrolase / diabetes / obesity / digestion / glycosidase / enzyme inhibition / flavonol / drug design / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


polysaccharide digestion / Digestion of dietary carbohydrate / alpha-amylase / carbohydrate catabolic process / alpha-amylase activity / chloride ion binding / carbohydrate metabolic process / calcium ion binding / extracellular space / extracellular exosome / extracellular region
Similarity search - Function
Alpha-amylase, C-terminal domain / Aamy_C / Alpha-amylase/branching enzyme, C-terminal all beta / Alpha amylase, C-terminal all-beta domain / Alpha amylase / Alpha amylase, catalytic domain / Glycosyl hydrolase, family 13, catalytic domain / Alpha-amylase domain / Golgi alpha-mannosidase II / Glycosyl hydrolase, all-beta ...Alpha-amylase, C-terminal domain / Aamy_C / Alpha-amylase/branching enzyme, C-terminal all beta / Alpha amylase, C-terminal all-beta domain / Alpha amylase / Alpha amylase, catalytic domain / Glycosyl hydrolase, family 13, catalytic domain / Alpha-amylase domain / Golgi alpha-mannosidase II / Glycosyl hydrolase, all-beta / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Chem-MYC / Pancreatic alpha-amylase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.2 Å
AuthorsWilliams, L.K. / Brayer, G.D.
CitationJournal: J.Med.Chem. / Year: 2012
Title: Order and disorder: differential structural impacts of myricetin and ethyl caffeate on human amylase, an antidiabetic target.
Authors: Williams, L.K. / Li, C. / Withers, S.G. / Brayer, G.D.
History
DepositionAug 23, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 24, 2012Provider: repository / Type: Initial release
Revision 1.1Dec 12, 2012Group: Database references
Revision 2.0Jul 29, 2020Group: Data collection / Derived calculations ...Data collection / Derived calculations / Polymer sequence / Structure summary
Category: chem_comp / entity ...chem_comp / entity / entity_poly / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _entity_poly.pdbx_seq_one_letter_code_can / _pdbx_entity_nonpoly.name / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Pancreatic alpha-amylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,5465
Polymers55,9311
Non-polymers6154
Water11,728651
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)52.129, 67.373, 129.929
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein / Sugars , 2 types, 2 molecules A

#1: Protein Pancreatic alpha-amylase / PA / 1 / 4-alpha-D-glucan glucanohydrolase


Mass: 55931.305 Da / Num. of mol.: 1 / Fragment: UNP residues 16-511
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: AMY2A / Production host: Komagataella pastoris (fungus) / References: UniProt: P04746, alpha-amylase
#2: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 4 types, 654 molecules

#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-MYC / 3,5,7-TRIHYDROXY-2-(3,4,5-TRIHYDROXYPHENYL)-4H-CHROMEN-4-ONE / 2-(3,4,5-TRIHYDROXYPHENYL)-3,5,7-TRIHYDROXY-4H-1-BENZOPYRAN-4-ONE / 3,3',4',5,5',7-HEXAHYDROXYFLAVONE / MYRICETIN / CANNABISCETIN / Myricetin


Mass: 318.235 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H10O8
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 651 / 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: 2.04 Å3/Da / Density % sol: 39.7 %
Crystal growTemperature: 300 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 60% MPD, 100 mM sodium cacodylate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 300K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.98 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Nov 15, 2007
RadiationMonochromator: Curved crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.2→43.31 Å / Num. all: 140097 / Num. obs: 140097 / % possible obs: 97.8 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3 / Redundancy: 4.6 %
Reflection shell
Resolution (Å)Diffraction-ID% possible all
1.2-1.26198.1
1.26-1.34197.6
1.34-1.43197.1
1.43-1.55196.5
1.55-1.7196.5
1.7-1.9197.8
1.9-2.19199.3
2.19-2.681100
2.68-3.79199.9
3.79-43.31197.5

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Processing

Software
NameClassification
Blu-Icedata collection
CNSrefinement
MOSFLMdata reduction
SCALAdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.2→43.31 Å / Occupancy max: 1 / Occupancy min: 0.4 / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.1984 7058 4.9 %RANDOM
Rwork0.1804 132955 --
obs-140013 97.6 %-
Solvent computationBsol: 49.518 Å2
Displacement parametersBiso max: 112.82 Å2 / Biso mean: 13.4103 Å2 / Biso min: 3.25 Å2
Baniso -1Baniso -2Baniso -3
1-0.913 Å20 Å20 Å2
2--0.299 Å20 Å2
3----1.212 Å2
Refinement stepCycle: LAST / Resolution: 1.2→43.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3946 0 39 651 4636
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.013
X-RAY DIFFRACTIONc_angle_d1.813
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2pca.par-fix
X-RAY DIFFRACTION3ion.param
X-RAY DIFFRACTION4nag.par-fix
X-RAY DIFFRACTION5water_rep.param

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