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- PDB-5kez: Selective and potent inhibition of the glycosidase human amylase ... -

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Basic information

Entry
Database: PDB / ID: 5kez
TitleSelective and potent inhibition of the glycosidase human amylase by the short and extremely compact peptide piHA from mRNA display
Components
  • ACE-DTY-PRO-TYR-SER-CYS-TRP-VAL-ARG-HIS-NH2
  • Pancreatic alpha-amylase
KeywordsHYDROLASE/HYDROLASE inhibitor / Amylase / Diabetes / Obesity / Glucosyl hydrolase / 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
Pancreatic alpha-amylase
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.83 Å
AuthorsCaner, S. / Brayer, G.D.
Funding support Canada, 1items
OrganizationGrant numberCountry
Canadian Glycomics Network/ Networks of Centres of Excellence Canada
CitationJournal: Cell Chem Biol / Year: 2017
Title: Rapid Discovery of Potent and Selective Glycosidase-Inhibiting De Novo Peptides.
Authors: Jongkees, S.A. / Caner, S. / Tysoe, C. / Brayer, G.D. / Withers, S.G. / Suga, H.
History
DepositionJun 10, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 29, 2017Provider: repository / Type: Initial release
Revision 2.0Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Polymer sequence / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / entity_poly / pdbx_initial_refinement_model / pdbx_struct_conn_angle / refine_hist / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_poly.pdbx_seq_one_letter_code_can / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _refine_hist.d_res_low / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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 / _struct_conn.ptnr2_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Pancreatic alpha-amylase
B: ACE-DTY-PRO-TYR-SER-CYS-TRP-VAL-ARG-HIS-NH2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,2434
Polymers57,1682
Non-polymers762
Water4,936274
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1890 Å2
ΔGint-37 kcal/mol
Surface area17560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.800, 75.840, 137.260
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#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: Protein/peptide ACE-DTY-PRO-TYR-SER-CYS-TRP-VAL-ARG-HIS-NH2


Mass: 1236.425 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 274 / 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: 2.42 Å3/Da / Density % sol: 49.18 %
Crystal growTemperature: 293 K / Method: evaporation / pH: 7.5 / Details: 53%-57% MPD, 0.1 M Na Cacodylate, pH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 1.03317 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 5, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03317 Å / Relative weight: 1
ReflectionResolution: 1.83→39.176 Å / Num. obs: 49017 / % possible obs: 99 % / Redundancy: 5.7 % / Rmerge(I) obs: 0.094 / Net I/σ(I): 14.5
Reflection shellResolution: 1.83→1.9 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.7896 / Mean I/σ(I) obs: 1.94 / % possible all: 99

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4X9Y

4x9y


Resolution: 1.83→39.176 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 20.14 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.208 2450 5 %
Rwork0.177 --
obs0.179 48983 99.1 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.83→39.176 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4035 0 2 274 4311
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074168
X-RAY DIFFRACTIONf_angle_d0.9155668
X-RAY DIFFRACTIONf_dihedral_angle_d12.2932401
X-RAY DIFFRACTIONf_chiral_restr0.058567
X-RAY DIFFRACTIONf_plane_restr0.006749
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.83-1.86520.33181330.2772512X-RAY DIFFRACTION99
1.8652-1.90330.29341340.25252546X-RAY DIFFRACTION98
1.9033-1.94470.28841320.22092524X-RAY DIFFRACTION98
1.9447-1.98990.23781350.2022564X-RAY DIFFRACTION99
1.9899-2.03970.25061350.19552553X-RAY DIFFRACTION99
2.0397-2.09480.22571350.18812571X-RAY DIFFRACTION100
2.0948-2.15640.25251350.19062563X-RAY DIFFRACTION100
2.1564-2.2260.25761340.19192549X-RAY DIFFRACTION99
2.226-2.30560.2261350.18752562X-RAY DIFFRACTION98
2.3056-2.39790.20221360.18452579X-RAY DIFFRACTION100
2.3979-2.5070.24231360.18672589X-RAY DIFFRACTION100
2.507-2.63910.20171360.182590X-RAY DIFFRACTION100
2.6391-2.80450.23821360.18882587X-RAY DIFFRACTION99
2.8045-3.02090.2231350.18982565X-RAY DIFFRACTION98
3.0209-3.32480.20691380.1812622X-RAY DIFFRACTION99
3.3248-3.80550.19891390.16182641X-RAY DIFFRACTION100
3.8055-4.79320.13661400.14122642X-RAY DIFFRACTION99
4.7932-39.18520.16741460.15272774X-RAY DIFFRACTION99

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