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- PDB-5va9: Human pancreatic alpha amylase in complex with peptide inhibitor ... -

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Basic information

Entry
Database: PDB / ID: 5va9
TitleHuman pancreatic alpha amylase in complex with peptide inhibitor piHA-L5(d10Y)
Components
  • Pancreatic alpha-amylase
  • Peptide Inhibitor piHA-L5(d10Y)
Keywordshydrolase/hydrolase inhibitor / amylase / diabetes / obesity / glucosyl hydrolase / peptide inhibitor complex / 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: 2.55 Å
AuthorsCaner, S. / Brayer, G.D.
Funding support Canada, 1items
OrganizationGrant numberCountry
GlycoNet: National Centres of ExcellenceDO-2 Canada
CitationJournal: Acs Chem.Biol. / Year: 2019
Title: Folding Then Binding vs Folding Through Binding in Macrocyclic Peptide Inhibitors of Human Pancreatic alpha-Amylase.
Authors: Goldbach, L. / Vermeulen, B.J.A. / Caner, S. / Liu, M. / Tysoe, C. / van Gijzel, L. / Yoshisada, R. / Trellet, M. / van Ingen, H. / Brayer, G.D. / Bonvin, A.M.J.J. / Jongkees, S.A.K.
History
DepositionMar 24, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 28, 2018Provider: repository / Type: Initial release
Revision 1.1Apr 18, 2018Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.detector
Revision 1.2Sep 25, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _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.year
Revision 2.0Oct 4, 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 / 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 / _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: Pancreatic alpha-amylase
C: Peptide Inhibitor piHA-L5(d10Y)
D: Peptide Inhibitor piHA-L5(d10Y)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,3368
Polymers116,1854
Non-polymers1514
Water3,801211
1
A: Pancreatic alpha-amylase
C: Peptide Inhibitor piHA-L5(d10Y)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,1684
Polymers58,0932
Non-polymers762
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2170 Å2
ΔGint-34 kcal/mol
Surface area17800 Å2
MethodPISA
2
B: Pancreatic alpha-amylase
D: Peptide Inhibitor piHA-L5(d10Y)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,1684
Polymers58,0932
Non-polymers762
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2180 Å2
ΔGint-33 kcal/mol
Surface area17640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)169.920, 169.920, 79.420
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11B-601-

HOH

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Components

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


Mass: 55931.305 Da / Num. of mol.: 2
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: Protein/peptide Peptide Inhibitor piHA-L5(d10Y)


Mass: 2161.384 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 211 / 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: 2.63 Å3/Da / Density % sol: 53.18 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: MPD 54%, 0.1 M sodium cacodylate.

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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: Jul 15, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 2.55→20 Å / Num. obs: 37249 / % possible obs: 96.9 % / Observed criterion σ(I): 2 / Redundancy: 11.38 % / CC1/2: 0.991 / Rmerge(I) obs: 0.224 / Net I/σ(I): 9.43
Reflection shellResolution: 2.55→2.62 Å / Redundancy: 9.45 % / Rmerge(I) obs: 0.916 / Mean I/σ(I) obs: 2.02 / Num. unique obs: 2574 / CC1/2: 0.795 / % possible all: 92

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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: 4X9Y

4x9y


Resolution: 2.55→19.595 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 23.16 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2297 1862 5 %random selection
Rwork0.1958 ---
obs0.1976 37238 97.13 %-
Solvent computationShrinkage radii: 0.7 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.55→19.595 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8202 0 4 211 8417
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0038458
X-RAY DIFFRACTIONf_angle_d0.60111492
X-RAY DIFFRACTIONf_dihedral_angle_d16.7893032
X-RAY DIFFRACTIONf_chiral_restr0.0731146
X-RAY DIFFRACTIONf_plane_restr0.0031520
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.55-2.61880.2991340.24962534X-RAY DIFFRACTION92
2.6188-2.69570.31141350.24662581X-RAY DIFFRACTION94
2.6957-2.78250.29061330.25592512X-RAY DIFFRACTION91
2.7825-2.88160.27321370.24542617X-RAY DIFFRACTION94
2.8816-2.99660.24971420.22522691X-RAY DIFFRACTION98
2.9966-3.13250.25041430.22342746X-RAY DIFFRACTION99
3.1325-3.29690.25421450.21872744X-RAY DIFFRACTION99
3.2969-3.50240.22491450.20732767X-RAY DIFFRACTION100
3.5024-3.7710.21721470.19232792X-RAY DIFFRACTION100
3.771-4.14730.22241470.17992778X-RAY DIFFRACTION99
4.1473-4.740.21371470.16072807X-RAY DIFFRACTION99
4.74-5.94410.1921500.17682848X-RAY DIFFRACTION100
5.9441-19.59540.19951570.16252959X-RAY DIFFRACTION99

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