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- PDB-1hx0: Structure of pig pancreatic alpha-amylase complexed with the "tru... -

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Basic information

Entry
Database: PDB / ID: 1hx0
TitleStructure of pig pancreatic alpha-amylase complexed with the "truncate" acarbose molecule (pseudotrisaccharide)
ComponentsALPHA AMYLASE (PPA)
KeywordsHYDROLASE / Alpha-amylase / inhibitor / carbohydrate / pancreas
Function / homology
Function and homology information


alpha-amylase / alpha-amylase activity / carbohydrate catabolic process / chloride ion binding / carbohydrate metabolic process / calcium ion binding / extracellular space
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
alpha-maltose / Pancreatic alpha-amylase
Similarity search - Component
Biological speciesSus scrofa (pig)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.38 Å
AuthorsQian, M. / Payan, F.
Citation
Journal: Biochemistry / Year: 2001
Title: Enzyme-catalyzed condensation reaction in a mammalian alpha-amylase. High-resolution structural analysis of an enzyme-inhibitor complex
Authors: Qian, M. / Nahoum, V. / Bonicel, J. / Bischoff, H. / Henrissat, B. / Payan, F.
#1: Journal: Eur.J.Biochem. / Year: 1996
Title: Crystal structure of pig pancreatic alpha-amylase isoenzyme II, in complex with the carbohydrate inhibitor acarbose
Authors: Gilles, C. / Astier, J.P. / Marchis-Mouren, G. / Cambillau, C. / Payan, F.
#2: Journal: Biochemistry / Year: 1994
Title: The active center of a mammalian alpha-amylase. Structure of the complex of a pancreatic alpha-amylase with a carbohydrate inhibitor refined to 2.2-A resolution
Authors: Qian, M. / Haser, R. / Buisson, G. / Duee, E. / Payan, F.
History
DepositionJan 11, 2001Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 8, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Atomic model / Version format compliance
Revision 2.0Jul 25, 2018Group: Atomic model / Data collection ...Atomic model / Data collection / Source and taxonomy / Structure summary
Category: atom_site / entity ...atom_site / entity / entity_src_gen / entity_src_nat
Item: _atom_site.occupancy / _entity.pdbx_mutation / _entity.src_method
Revision 3.0Dec 25, 2019Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Polymer sequence
Category: chem_comp / entity_poly ...chem_comp / entity_poly / pdbx_struct_mod_residue / struct_conn / struct_ref_seq_dif
Item: _chem_comp.type / _entity_poly.pdbx_seq_one_letter_code_can ..._chem_comp.type / _entity_poly.pdbx_seq_one_letter_code_can / _pdbx_struct_mod_residue.parent_comp_id / _struct_conn.pdbx_leaving_atom_flag
Revision 4.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_alt_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.occupancy / _atom_site.type_symbol / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_alt_id / _atom_site_anisotrop.pdbx_label_asym_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.value
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 4.1Oct 25, 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 4.2Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ALPHA AMYLASE (PPA)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,69120
Polymers55,4731
Non-polymers2,21819
Water16,592921
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)69.280, 113.550, 117.160
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 , 1 types, 1 molecules A

#1: Protein ALPHA AMYLASE (PPA)


Mass: 55472.828 Da / Num. of mol.: 1 / Mutation: Q16PCA
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sus scrofa (pig) / Tissue: PANCREAS / Production host: Escherichia coli (E. coli) / References: UniProt: P00690, alpha-amylase

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Sugars , 2 types, 2 molecules

#2: Polysaccharide 4,6-dideoxy-4-{[(1S,4R,5S,6S)-4,5,6-trihydroxy-3-(hydroxymethyl)cyclohex-2-en-1-yl]amino}-alpha-D- ...4,6-dideoxy-4-{[(1S,4R,5S,6S)-4,5,6-trihydroxy-3-(hydroxymethyl)cyclohex-2-en-1-yl]amino}-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-4,6-dideoxy-4-{[(1S,4R,5S,6S)-4,5,6-trihydroxy-3-(hydroxymethyl)cyclohex-2-en-1-yl]amino}-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose


Type: oligosaccharide / Mass: 948.914 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
WURCS=2.0/3,4,3/[a2122h-1a_1-5][a2122m-1a_1-5][a2122m-1a_1-5_4*NC^SC^SC^SC^RCCO/7=^ZC$3/6O/5O/4O]/1-2-1-3/a4-b1_b4n2-c1n1*1OC^RC^RC^SC^SN*2/6C=^ZCCO/10$3/5O/4O_c4-d1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(4+1)][a-D-6-deoxy-Glcp4N]{[(4+1)][non_ch_ring]{[(4+1)][a-D-Glcp]{[(4+1)][a-D-6-deoxy-Glcp4N]{[(4+1)][<C7O4>]{}}}}}}LINUCSPDB-CARE
#3: Polysaccharide alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose / alpha-maltose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: alpha-maltose
DescriptorTypeProgram
DGlcpa1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1a_1-5]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-Glcp]{[(4+1)][a-D-Glcp]{}}LINUCSPDB-CARE

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Non-polymers , 4 types, 938 molecules

#4: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / 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: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C2H6O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 921 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY
Nonpolymer detailsRESIDUE GLC 1993 AND GBC 2993 ARE IN ALTERNATE CONFORMATIONS OF EACH OTHER.

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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: 4.15 Å3/Da / Density % sol: 70.38 %
Crystal growTemperature: 277 K / Method: batch / pH: 8.5 / Details: CaCl2, pH 8.5, batch, temperature 277K
Crystal grow
*PLUS
Details: Qian, M., (1993) J. Mol. Biol., 232, 785.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 20, 1999
RadiationMonochromator: bouble-diamond crystal (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 1.38→35 Å / Num. all: 189616 / Num. obs: 184003 / % possible obs: 97.04 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 2.8 % / Biso Wilson estimate: 15.9 Å2 / Rmerge(I) obs: 0.067 / Net I/σ(I): 13.1
Reflection shellResolution: 1.38→1.42 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.581 / Mean I/σ(I) obs: 1.93 / Num. unique all: 16627 / % possible all: 96.13
Reflection
*PLUS
Num. measured all: 507677
Reflection shell
*PLUS
% possible obs: 96.13 % / Rmerge(I) obs: 0.451 / Mean I/σ(I) obs: 2.5

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Processing

Software
NameClassification
DENZOdata reduction
SCALAdata scaling
AMoREphasing
SHELXL-97refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1PPI

1ppi


Resolution: 1.38→35 Å / Cross valid method: throughout FREE R / σ(F): 1 / σ(I): 1 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.1302 2938 -RANDOM
Rwork0.1079 ---
all0.1083 184003 --
obs0.1083 184003 97 %-
Refinement stepCycle: LAST / Resolution: 1.38→35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3911 0 152 921 4984
Software
*PLUS
Name: SHELXL-97 / Classification: refinement
Refinement
*PLUS
σ(F): 1
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.013
X-RAY DIFFRACTIONs_angle_d0.03
X-RAY DIFFRACTIONs_angle_deg
X-RAY DIFFRACTIONs_dihedral_angle_d
X-RAY DIFFRACTIONs_improper_angle_d
X-RAY DIFFRACTIONs_mcbond_it
X-RAY DIFFRACTIONs_scbond_it
X-RAY DIFFRACTIONs_mcangle_it
X-RAY DIFFRACTIONs_scangle_it
LS refinement shell
*PLUS
Highest resolution: 1.38 Å / Lowest resolution: 1.42 Å / Num. reflection obs: 47628

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