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- PDB-6ocn: Montbretin A analogue M06-MbA in complex with Human pancreatic al... -

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Basic information

Entry
Database: PDB / ID: 6ocn
TitleMontbretin A analogue M06-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 / Glycosyl hydrolase, all-beta / Glycoside hydrolase superfamily
Similarity search - Domain/homology
Chem-ZXY / Pancreatic alpha-amylase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.147 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 25, 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

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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)56,8475
Polymers55,9311
Non-polymers9154
Water9,548530
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)52.310, 68.020, 130.530
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
#2: 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 , 4 types, 533 molecules

#3: Chemical ChemComp-ZXY / N-(3-{[2-(3,4-dihydroxyphenyl)-5,7-dihydroxy-4-oxo-4H-1-benzopyran-3-yl]oxy}propyl)-1-[(2E)-3-(3,4-dihydroxyphenyl)prop-2-enoyl]-L-prolinamide / Montbretin A analogue M06-MbA


Mass: 618.587 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C32H30N2O11
#4: Chemical ChemComp-CL / CHLORIDE ION


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


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


Mass: 18.015 Da / Num. of mol.: 530 / 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: 2.07 Å3/Da / Density % sol: 40.53 %
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: 0.9795 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: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.147→34.01 Å / Num. obs: 162652 / % possible obs: 97.5 % / Redundancy: 8.4 % / Biso Wilson estimate: 10.74 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 17.54
Reflection shellResolution: 1.147→1.18 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.4 / Num. unique obs: 8973 / CC1/2: 0.919 / % possible all: 73.4

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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: 1.147→34.01 Å / SU ML: 0.07 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 8.52
RfactorNum. reflection% reflection
Rfree0.1166 8105 4.98 %
Rwork0.0988 --
obs0.0997 162649 97.51 %
Solvent computationShrinkage radii: 0.7 Å / VDW probe radii: 1.1 Å
Refinement stepCycle: LAST / Resolution: 1.147→34.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3960 0 47 533 4540
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0094278
X-RAY DIFFRACTIONf_angle_d1.1245849
X-RAY DIFFRACTIONf_dihedral_angle_d14.7561560
X-RAY DIFFRACTIONf_chiral_restr0.099587
X-RAY DIFFRACTIONf_plane_restr0.009777
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.1471-1.16010.21991220.172705X-RAY DIFFRACTION51
1.1601-1.17380.13492400.12024779X-RAY DIFFRACTION91
1.1738-1.18810.13922840.10525115X-RAY DIFFRACTION98
1.1881-1.20310.12812600.09735207X-RAY DIFFRACTION100
1.2031-1.21890.11882780.09925209X-RAY DIFFRACTION100
1.2189-1.23560.12742750.09315222X-RAY DIFFRACTION100
1.2356-1.25330.11562730.09165172X-RAY DIFFRACTION100
1.2533-1.2720.10852750.09035236X-RAY DIFFRACTION99
1.272-1.29190.12052780.08835174X-RAY DIFFRACTION99
1.2919-1.31310.12122630.08575147X-RAY DIFFRACTION98
1.3131-1.33570.10652790.08115221X-RAY DIFFRACTION100
1.3357-1.360.11212740.0815243X-RAY DIFFRACTION100
1.36-1.38620.10712770.07975237X-RAY DIFFRACTION100
1.3862-1.41440.11222700.07975242X-RAY DIFFRACTION100
1.4144-1.44520.10512820.07785211X-RAY DIFFRACTION100
1.4452-1.47880.10362690.07585224X-RAY DIFFRACTION99
1.4788-1.51580.10342680.07565156X-RAY DIFFRACTION98
1.5158-1.55680.10342770.07695217X-RAY DIFFRACTION100
1.5568-1.60260.10692740.07275274X-RAY DIFFRACTION100
1.6026-1.65430.09962810.07395277X-RAY DIFFRACTION100
1.6543-1.71340.10592780.08045259X-RAY DIFFRACTION100
1.7134-1.7820.10912730.08355259X-RAY DIFFRACTION99
1.782-1.86310.10192800.08795241X-RAY DIFFRACTION99
1.8631-1.96140.09782750.09045233X-RAY DIFFRACTION99
1.9614-2.08420.10952810.09465312X-RAY DIFFRACTION100
2.0842-2.24510.10572800.09175298X-RAY DIFFRACTION100
2.2451-2.4710.11442830.0995351X-RAY DIFFRACTION100
2.471-2.82840.13582780.11375315X-RAY DIFFRACTION99
2.8284-3.56290.12642840.11765443X-RAY DIFFRACTION100
3.5629-34.02490.1282940.12285565X-RAY DIFFRACTION99

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