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- PDB-6obx: Montbretin A analogue M10-MbA in complex with Human pancreatic al... -

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Basic information

Entry
Database: PDB / ID: 6obx
TitleMontbretin A analogue M10-MbA in complex with Human pancreatic alpha-amylase
ComponentsPancreatic alpha-amylase
KeywordsHYDROLASE / Amylase / Diabetes / Obesity / Glucosyl hydrolase
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-ZXU / Pancreatic alpha-amylase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å
AuthorsCaner, S. / Brayer, G.D.
Funding support Canada, 1items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR)CIHR MOP-111082 Canada
CitationJournal: Chem Sci / Year: 2019
Title: Synthesis of montbretin A analogues yields potent competitive inhibitors of human pancreatic alpha-amylase.
Authors: Tysoe, C.R. / Caner, S. / Calvert, M.B. / Win-Mason, A. / Brayer, G.D. / Withers, S.G.
History
DepositionMar 21, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 12, 2020Provider: repository / Type: Initial release
Revision 1.1Apr 15, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_id_ISSN / _citation.journal_volume ..._citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _entity.pdbx_description ..._chem_comp.name / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _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 / _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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Oct 11, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)57,0316
Polymers55,9311
Non-polymers1,1005
Water9,296516
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)52.420, 68.220, 130.330
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
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: AMY2A / Organ: Pancreas / Production host: Komagataella pastoris (fungus) / References: UniProt: P04746, alpha-amylase
#6: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


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 , 5 types, 520 molecules

#2: Chemical ChemComp-CL / CHLORIDE ION


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


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-ZXU / N-(3-{[2-(3,4-dihydroxyphenyl)-5,7-dihydroxy-4-oxo-4H-1-benzopyran-3-yl]oxy}propyl)-Nalpha-[(2E)-3-(3,4-dihydroxyphenyl )prop-2-enoyl]-L-tyrosinamide / synthetic Montbretin A analogue


Mass: 684.645 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C36H32N2O12
#5: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 516 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 2.08 Å3/Da / Density % sol: 40.96 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 100 mM sodium cacodylate, 52-58% MPD / PH range: 7.0-7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 0.97946 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 26, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 1.3→36.6 Å / Num. obs: 113320 / % possible obs: 98.1 % / Redundancy: 8.6 % / Net I/σ(I): 19.68
Reflection shellResolution: 1.3→1.33 Å / Num. unique obs: 8212

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5U3A

5u3a


Resolution: 1.3→36.6 Å / SU ML: 0.08 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 9.52
RfactorNum. reflection% reflection
Rfree0.1227 5668 5 %
Rwork0.0987 --
obs0.0999 113294 98.07 %
Solvent computationShrinkage radii: 0.5 Å / VDW probe radii: 0.9 Å
Refinement stepCycle: LAST / Resolution: 1.3→36.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3946 0 74 517 4537
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0094255
X-RAY DIFFRACTIONf_angle_d1.135813
X-RAY DIFFRACTIONf_dihedral_angle_d14.8731539
X-RAY DIFFRACTIONf_chiral_restr0.097583
X-RAY DIFFRACTIONf_plane_restr0.009768
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.2999-1.31470.12761850.09333468X-RAY DIFFRACTION96
1.3147-1.33020.12541880.08323518X-RAY DIFFRACTION99
1.3302-1.34640.12971870.08193566X-RAY DIFFRACTION98
1.3464-1.36340.14151920.0823570X-RAY DIFFRACTION99
1.3634-1.38140.1211830.08253509X-RAY DIFFRACTION97
1.3814-1.40030.12221910.08583560X-RAY DIFFRACTION99
1.4003-1.42030.12911830.08333567X-RAY DIFFRACTION98
1.4203-1.44150.11611890.08083523X-RAY DIFFRACTION99
1.4415-1.4640.12971810.08323573X-RAY DIFFRACTION98
1.464-1.4880.13571900.083553X-RAY DIFFRACTION97
1.488-1.51370.11091740.07973422X-RAY DIFFRACTION95
1.5137-1.54120.12221900.07853574X-RAY DIFFRACTION98
1.5412-1.57090.12311890.07943572X-RAY DIFFRACTION99
1.5709-1.60290.12251830.07733583X-RAY DIFFRACTION98
1.6029-1.63780.10821930.07633585X-RAY DIFFRACTION98
1.6378-1.67590.12011850.07873598X-RAY DIFFRACTION99
1.6759-1.71780.11121960.08263628X-RAY DIFFRACTION99
1.7178-1.76420.11981880.08113602X-RAY DIFFRACTION99
1.7642-1.81610.10311870.0853587X-RAY DIFFRACTION98
1.8161-1.87480.12561870.08663489X-RAY DIFFRACTION96
1.8748-1.94180.10881900.08713585X-RAY DIFFRACTION98
1.9418-2.01950.11531870.0883643X-RAY DIFFRACTION100
2.0195-2.11140.10721940.09093637X-RAY DIFFRACTION99
2.1114-2.22270.1141920.0893649X-RAY DIFFRACTION99
2.2227-2.36190.11891930.0953638X-RAY DIFFRACTION99
2.3619-2.54430.12331930.10153641X-RAY DIFFRACTION99
2.5443-2.80020.1381900.1093513X-RAY DIFFRACTION95
2.8002-3.20520.13031920.11683711X-RAY DIFFRACTION99
3.2052-4.03740.12121910.11013746X-RAY DIFFRACTION99
4.0374-36.65860.13482050.13293816X-RAY DIFFRACTION97

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