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- PDB-1jfh: STRUCTURE OF A PANCREATIC ALPHA-AMYLASE BOUND TO A SUBSTRATE ANAL... -

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Basic information

Entry
Database: PDB / ID: 1jfh
TitleSTRUCTURE OF A PANCREATIC ALPHA-AMYLASE BOUND TO A SUBSTRATE ANALOGUE AT 2.03 ANGSTROM RESOLUTION
ComponentsALPHA-AMYLASE
KeywordsHYDROLASE / O-GLYCOSYL / ALPHA-AMYLASE / METHYL 4 / 4'-DITHIO-ALPHA-MALTOTRIOSIDE
Function / homology
Function and homology information


alpha-amylase / carbohydrate catabolic process / alpha-amylase activity / 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
: / Pancreatic alpha-amylase
Similarity search - Component
Biological speciesSus scrofa (pig)
MethodX-RAY DIFFRACTION / Resolution: 2.03 Å
AuthorsQian, M. / Payan, F.
Citation
Journal: Protein Sci. / Year: 1997
Title: Structure of a pancreatic alpha-amylase bound to a substrate analogue at 2.03 A resolution.
Authors: Qian, M. / Spinelli, S. / Driguez, H. / 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: Protein Sci. / Year: 1995
Title: Carbohydrate Binding Sites in a Pancreatic Alpha-Amylase-Substrate Complex, Derived from X-Ray Structure Analysis at 2.1 A Resolution
Authors: Qian, M. / Haser, R. / Payan, F.
#3: 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.
#4: Journal: J.Mol.Biol. / Year: 1993
Title: Structure and Molecular Model Refinement of Pig Pancreatic Alpha-Amylase at 2.1 A Resolution
Authors: Qian, M. / Haser, R. / Payan, F.
History
DepositionSep 19, 1997Processing site: BNL
Revision 1.0Dec 2, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 2.0Dec 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 / _struct_ref_seq_dif.details
Revision 3.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / 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_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_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ALPHA-AMYLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,8607
Polymers55,4331
Non-polymers1,4276
Water6,900383
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)56.300, 87.800, 103.400
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: 55432.762 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: COMPLEXED WITH METHYL 4,4'-DITHIO-ALPHA-MALTOTRIOSIDE
Source: (natural) Sus scrofa (pig) / Organ: PANCREAS / References: UniProt: P00690, alpha-amylase

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Sugars , 2 types, 3 molecules

#2: Polysaccharide 4-S-methyl-4-thio-alpha-D-glucopyranose-(1-4)-methyl 4-thio-alpha-D-glucopyranoside


Type: oligosaccharide / Mass: 402.481 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
WURCS=2.0/2,2,1/[a2122h-1a_1-5_1*OC][a2122h-1a_1-5_4*SC]/1-2/a4-b1*S*WURCSPDB2Glycan 1.1.0
[][methyl]{[(1+1)][a-D-Glcp4SH]{[(4+S)][a-D-Glcp4SMe]{}}}LINUCSPDB-CARE
#3: Polysaccharide alpha-D-glucopyranose-(1-4)-1,4-dithio-alpha-D-glucopyranose


Type: oligosaccharide / Mass: 374.428 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
WURCS=2.0/2,2,1/[a2122h-1a_1-5_1*S][a2122h-1a_1-5]/1-2/a4-b1*S*WURCSPDB2Glycan 1.1.0
[][a-D-Glcp1SH4SH]{[(4+S)][a-D-Glcp]{}}LINUCSPDB-CARE

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Non-polymers , 4 types, 386 molecules

#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-HG / MERCURY (II) ION / Mercury (element)


Mass: 200.590 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Hg
#6: Chemical ChemComp-CA / CALCIUM ION


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


Mass: 18.015 Da / Num. of mol.: 383 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.3 Å3/Da / Density % sol: 45 %
Crystal grow
*PLUS
Method: unknown

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Data collection

Diffraction sourceWavelength: 1.5418
DetectorType: MAR scanner 180 mm plate / Detector: IMAGE PLATE
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionNum. obs: 33718 / % possible obs: 99.4 % / Observed criterion σ(I): 1 / Redundancy: 9.5 % / Rmerge(I) obs: 0.057
Reflection
*PLUS
Highest resolution: 2.03 Å / Num. measured all: 322368
Reflection shell
*PLUS
% possible obs: 99.8 % / Rmerge(I) obs: 0.139

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Processing

Software
NameVersionClassification
DENZOdata reduction
X-PLOR3.843model building
X-PLOR3.843refinement
X-PLOR3.843phasing
RefinementResolution: 2.03→35 Å / σ(F): 0
RfactorNum. reflection
Rfree0.185 -
Rwork0.16 -
obs0.16 33421
Refine analyzeLuzzati coordinate error obs: 0.2 Å
Refinement stepCycle: LAST / Resolution: 2.03→35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3908 0 71 384 4363
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.01
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.4
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Version: 3.843 / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS

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