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- PDB-26wd: Structure of honeybee alpha-amylase belonging to glycoside hydrol... -

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Basic information

Entry
Database: PDB / ID: 26wd
TitleStructure of honeybee alpha-amylase belonging to glycoside hydrolase family 13 subfamily 15
ComponentsAlpha-amylase
KeywordsHYDROLASE / Inhibitor / alpha-Amylase / Acarbose / Honey
Function / homology
Function and homology information


alpha-amylase / alpha-amylase activity / carbohydrate metabolic process / metal ion binding
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
beta-maltose / ACARBOSE DERIVED HEXASACCHARIDE / Chem-ACI / beta-D-glucopyranose / Alpha-amylase
Similarity search - Component
Biological speciesApis mellifera (honey bee)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsSaburi, W. / Takahashi, Y. / Takei, S. / Ose, T. / Mori, H.
Funding support Japan, 1items
OrganizationGrant numberCountry
Not funded Japan
CitationJournal: Molecules / Year: 2026
Title: Structure and Function of Honeybee alpha-Amylase of Glycoside Hydrolase Family 13 Subfamily 15.
Authors: Saburi, W. / Takahashi, Y. / Takei, S. / Ose, T. / Mori, H.
History
DepositionMay 18, 2026Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 26, 2026Provider: repository / Type: Initial release

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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)57,34428
Polymers54,0791
Non-polymers3,26627
Water2,630146
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7000 Å2
ΔGint43 kcal/mol
Surface area17030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.729, 89.729, 122.193
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-619-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Alpha-amylase


Mass: 54078.516 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Apis mellifera (honey bee) / Gene: LOC406114, 406114 / Production host: Komagataella pastoris (fungus) / References: UniProt: A0A7M6W876, alpha-amylase

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Sugars , 4 types, 4 molecules

#2: Polysaccharide alpha-D-glucopyranose-(1-4)-beta-D-glucopyranose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: beta-maltose
DescriptorTypeProgram
DGlcpa1-4DGlcpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2122h-1b_1-5][a2122h-1a_1-5]/1-2/a4-b1WURCSPDB2Glycan 1.1.0
[][b-D-Glcp]{[(4+1)][a-D-Glcp]{}}LINUCSPDB-CARE
#5: 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: obtained synthetically / 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
#7: Sugar ChemComp-AAO / ACARBOSE DERIVED HEXASACCHARIDE / 4,6-DIDEOXY-4-{[4-[(4-O-HEXOPYRANOSYLHEXOPYRANOSYL)OXY]-5,6-DIHYDROXY-3-(HYDROXYMETHYL)CYCLOHEX-2-EN-1-YL]AMINO}HEXOPYRANOSYL-(1->4)HEXOPYRANOSYL-(1->4)HEXOPYRANOSE


Type: saccharide / Mass: 969.886 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C37H63NO28 / Feature type: SUBJECT OF INVESTIGATION
#8: Sugar ChemComp-BGC / beta-D-glucopyranose / beta-D-glucose / D-glucose / glucose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H12O6
IdentifierTypeProgram
DGlcpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-glucopyranoseCOMMON NAMEGMML 1.0
b-D-GlcpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 6 types, 169 molecules

#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-ACI / 6-AMINO-4-HYDROXYMETHYL-CYCLOHEX-4-ENE-1,2,3-TRIOL


Mass: 175.182 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H13NO4
#9: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#10: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#11: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 146 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY

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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: 2.27 Å3/Da / Density % sol: 45.91 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 10 mM acarbose, 0.1 M imidazole-HCl (pH 8.0), 40% PEG400

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL45XU / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 5, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 40052 / % possible obs: 99.8 % / Redundancy: 52.8 % / CC1/2: 0.997 / Net I/σ(I): 13.7
Reflection shellResolution: 1.9→2.01 Å / Num. unique obs: 6355 / CC1/2: 0.586

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: AlphaFold

Resolution: 1.9→44.86 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 20.56 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2297 1998 5 %
Rwork0.2031 --
obs0.2044 39945 99.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.9→44.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3812 0 198 146 4156
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0034097
X-RAY DIFFRACTIONf_angle_d0.6255526
X-RAY DIFFRACTIONf_dihedral_angle_d8.09616
X-RAY DIFFRACTIONf_chiral_restr0.046583
X-RAY DIFFRACTIONf_plane_restr0.006710
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.950.33981410.30252675X-RAY DIFFRACTION100
1.95-20.31011400.28882661X-RAY DIFFRACTION100
2-2.060.2891400.26592657X-RAY DIFFRACTION100
2.06-2.130.29081400.2372661X-RAY DIFFRACTION100
2.13-2.20.22221410.21952694X-RAY DIFFRACTION100
2.2-2.290.23691410.21042672X-RAY DIFFRACTION100
2.29-2.390.23651420.19182685X-RAY DIFFRACTION100
2.39-2.520.20781400.18512687X-RAY DIFFRACTION100
2.52-2.680.21561430.17852708X-RAY DIFFRACTION100
2.68-2.880.23571430.18242710X-RAY DIFFRACTION100
2.88-3.170.20091430.17272727X-RAY DIFFRACTION100
3.18-3.630.1941460.17532744X-RAY DIFFRACTION100
3.63-4.580.20191450.16732776X-RAY DIFFRACTION100

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