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- PDB-5emy: Human Pancreatic Alpha-Amylase in complex with the mechanism base... -

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Basic information

Entry
Database: PDB / ID: 5emy
TitleHuman Pancreatic Alpha-Amylase in complex with the mechanism based inactivator glucosyl epi-cyclophellitol
ComponentsPancreatic 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
Chem-5QP / Pancreatic alpha-amylase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.231 Å
AuthorsCaner, S. / Brayer, G.D.
Funding support Canada, 1items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR)CIHR MOP-111082 Canada
CitationJournal: Febs Lett. / Year: 2016
Title: Glucosyl epi-cyclophellitol allows mechanism-based inactivation and structural analysis of human pancreatic alpha-amylase.
Authors: Caner, S. / Zhang, X. / Jiang, J. / Chen, H.M. / Nguyen, N.T. / Overkleeft, H. / Brayer, G.D. / Withers, S.G.
History
DepositionNov 6, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 6, 2016Provider: repository / Type: Initial release
Revision 2.0Jan 8, 2020Group: Author supporting evidence / Database references ...Author supporting evidence / Database references / Derived calculations / Polymer sequence
Category: citation / entity_poly ...citation / entity_poly / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _entity_poly.pdbx_seq_one_letter_code_can ..._citation.journal_id_CSD / _entity_poly.pdbx_seq_one_letter_code_can / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 3.0Jul 29, 2020Group: Atomic model / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_site / struct_site_gen
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _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_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _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 3.1Sep 27, 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)56,3474
Polymers55,9311
Non-polymers4163
Water10,070559
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)52.330, 68.180, 130.380
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
Details: The residue (XEP) is a modified Aspartate with the complexed Glucosyl-epi-cyclophellitol
Source: (gene. exp.) Homo sapiens (human) / Gene: AMY2A / Organ: Pancreas / Production host: Komagataella pastoris (fungus) / References: UniProt: P04746, alpha-amylase
#2: Sugar ChemComp-5QP / (1R,2R,3S,5R,6S)-2,3,5-trihydroxy-6-(hydroxymethyl)cyclohexyl alpha-D-glucopyranoside / (2~{R},3~{S},4~{S},5~{R},6~{S})-2-(hydroxymethyl)-6-[(1~{R},2~{S},3~{R},5~{S},6~{R})-2-(hydroxymethyl)-3,5,6-tris(oxida nyl)cyclohexyl]oxy-oxane-3,4,5-triol / gluosyl epi-cyclophellitol (bound form) / (1R,2R,3S,5R,6S)-2,3,5-trihydroxy-6-(hydroxymethyl)cyclohexyl alpha-D-glucoside / (1R,2R,3S,5R,6S)-2,3,5-trihydroxy-6-(hydroxymethyl)cyclohexyl D-glucoside / (1R,2R,3S,5R,6S)-2,3,5-trihydroxy-6-(hydroxymethyl)cyclohexyl glucoside


Type: D-saccharide / Mass: 340.324 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H24O10
#3: Chemical ChemComp-CL / CHLORIDE ION


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


Mass: 18.015 Da / Num. of mol.: 559 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsThe authors state that the starting material of the ligand is Glucosyl-epi-cyclophellitol

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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: 40.98 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 100 mM sodium cacodylate, 58% MPD, obtained crystals were soaked in 100mM glucosyl epi-cyclophellitol solution and incubated for up to two weeks to allow complex formation.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.97946 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 16, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 1.23→36.65 Å / Num. all: 134773 / Num. obs: 134741 / % possible obs: 99.5 % / Observed criterion σ(I): 2 / Redundancy: 5.4 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 19.54
Reflection shellResolution: 1.23→1.26 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.75 / Mean I/σ(I) obs: 2.02 / % possible all: 94

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Processing

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

4x9y


Resolution: 1.231→36.648 Å / SU ML: 0.1 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 12.52 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1421 6738 5 %
Rwork0.1189 --
obs0.1201 134741 99.49 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.231→36.648 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3946 0 25 559 4530
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074125
X-RAY DIFFRACTIONf_angle_d1.0445618
X-RAY DIFFRACTIONf_dihedral_angle_d13.3151470
X-RAY DIFFRACTIONf_chiral_restr0.087579
X-RAY DIFFRACTIONf_plane_restr0.007734
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.2312-1.24520.27821960.26513705X-RAY DIFFRACTION87
1.2452-1.25990.22892210.20454208X-RAY DIFFRACTION100
1.2599-1.27520.20032220.19044215X-RAY DIFFRACTION100
1.2752-1.29140.20782230.16624246X-RAY DIFFRACTION100
1.2914-1.30840.18852240.16354249X-RAY DIFFRACTION100
1.3084-1.32630.16772230.15234245X-RAY DIFFRACTION100
1.3263-1.34520.18772230.14634224X-RAY DIFFRACTION100
1.3452-1.36530.15862230.13694246X-RAY DIFFRACTION100
1.3653-1.38670.16892240.13424259X-RAY DIFFRACTION100
1.3867-1.40940.16192240.12934250X-RAY DIFFRACTION100
1.4094-1.43370.14612230.12414244X-RAY DIFFRACTION100
1.4337-1.45980.16112250.11574270X-RAY DIFFRACTION100
1.4598-1.48790.15512240.11024254X-RAY DIFFRACTION100
1.4879-1.51820.14932240.10654246X-RAY DIFFRACTION100
1.5182-1.55120.13182240.10234259X-RAY DIFFRACTION100
1.5512-1.58730.13762250.09754276X-RAY DIFFRACTION100
1.5873-1.6270.12272240.09754255X-RAY DIFFRACTION100
1.627-1.6710.12922240.0944259X-RAY DIFFRACTION100
1.671-1.72020.12242250.09374280X-RAY DIFFRACTION100
1.7202-1.77570.1132240.09344261X-RAY DIFFRACTION100
1.7757-1.83920.11962270.09654302X-RAY DIFFRACTION100
1.8392-1.91280.11772250.0984275X-RAY DIFFRACTION100
1.9128-1.99980.12822270.1034322X-RAY DIFFRACTION100
1.9998-2.10530.13922260.10514287X-RAY DIFFRACTION100
2.1053-2.23720.12442260.10254306X-RAY DIFFRACTION100
2.2372-2.40990.12582280.10684328X-RAY DIFFRACTION100
2.4099-2.65230.12782290.11254348X-RAY DIFFRACTION100
2.6523-3.03590.13582300.11944358X-RAY DIFFRACTION100
3.0359-3.82430.13952320.12184422X-RAY DIFFRACTION100
3.8243-36.6640.16212430.14294604X-RAY DIFFRACTION100

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