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- PDB-5wvx: Crystal Structure of bifunctional Kunitz type Trypsin /amylase in... -

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Basic information

Entry
Database: PDB / ID: 5wvx
TitleCrystal Structure of bifunctional Kunitz type Trypsin /amylase inhibitor (AMTIN) from the tubers of Alocasia macrorrhiza
ComponentsTrypsin/chymotrypsin inhibitor
KeywordsHYDROLASE INHIBITOR / Kunitz type Trypsin inhibitor / Alpha amylase inhibitor
Function / homology
Function and homology information


negative regulation of peptidase activity / serine-type endopeptidase inhibitor activity
Similarity search - Function
Proteinase inhibitor A/B / Proteinase inhibitor I3, Kunitz legume / Trypsin and protease inhibitor / Soybean trypsin inhibitor (Kunitz) family of protease inhibitors / Kunitz inhibitor STI-like superfamily
Similarity search - Domain/homology
CITRIC ACID / 2-acetamido-2-deoxy-beta-D-galactopyranose / Trypsin/chymotrypsin inhibitor
Similarity search - Component
Biological speciesAlocasia macrorrhizos (giant taro)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3.003 Å
AuthorsPalayam, M. / Radhakrishnan, M. / Lakshminarayanan, K. / Balu, K.E. / Ganapathy, J. / Krishnasamy, G.
CitationJournal: Int. J. Biol. Macromol. / Year: 2018
Title: Structural insights into a multifunctional inhibitor, 'AMTIN' from tubers of Alocasia macrorrhizos and its possible role in dengue protease (NS2B-NS3) inhibition.
Authors: Palayam, M. / Ganapathy, J. / Balu, K.E. / Pennathur, G. / Krishnasamy, G.
History
DepositionDec 29, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 13, 2018Provider: repository / Type: Initial release
Revision 1.1Jun 24, 2020Group: Advisory / Data collection / Category: chem_comp / database_PDB_caveat / Item: _chem_comp.type / _database_PDB_caveat.text
Revision 1.2Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _chem_comp.name / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Nov 22, 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

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Assembly

Deposited unit
A: Trypsin/chymotrypsin inhibitor
B: Trypsin/chymotrypsin inhibitor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,4136
Polymers39,5862
Non-polymers8274
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2430 Å2
ΔGint-7 kcal/mol
Surface area15300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.340, 84.340, 57.980
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41

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Components

#1: Protein Trypsin/chymotrypsin inhibitor


Mass: 19793.139 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Alocasia macrorrhizos (giant taro) / References: UniProt: P35812
#2: Sugar ChemComp-NGA / 2-acetamido-2-deoxy-beta-D-galactopyranose / N-acetyl-beta-D-galactosamine / 2-acetamido-2-deoxy-beta-D-galactose / 2-acetamido-2-deoxy-D-galactose / 2-acetamido-2-deoxy-galactose / N-ACETYL-D-GALACTOSAMINE / N-Acetylgalactosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGalpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-galactopyranosamineCOMMON NAMEGMML 1.0
b-D-GalpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GalNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Chemical ChemComp-CIT / CITRIC ACID / Citric acid


Mass: 192.124 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H8O7

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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: 2.6 Å3/Da / Density % sol: 52.78 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4 / Details: Ammonium sulfate and citrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.54 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Aug 19, 2015
RadiationMonochromator: CuK / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 3.003→84.34 Å / Num. obs: 8256 / % possible obs: 99.71 % / Redundancy: 5 % / CC1/2: 0.991 / Rmerge(I) obs: 0.05494 / Net I/σ(I): 14.36
Reflection shellResolution: 3.003→3.111 Å

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
iMOSFLMdata reduction
Aimlessdata scaling
EPMRphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1AVA

1ava


Resolution: 3.003→84.34 Å / Cross valid method: FREE R-VALUE / σ(F): 44.35 / Phase error: 30.16
RfactorNum. reflection% reflection
Rfree0.3113 817 9.9 %
Rwork0.2786 --
obs0.2982 8256 99.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.003→84.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2244 0 54 0 2298
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0042337
X-RAY DIFFRACTIONf_angle_d0.8173173
X-RAY DIFFRACTIONf_dihedral_angle_d7.1981384
X-RAY DIFFRACTIONf_chiral_restr0.049361
X-RAY DIFFRACTIONf_plane_restr0.008424
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.0062-3.19450.38511330.30021217X-RAY DIFFRACTION89
3.1945-3.44110.3841330.29761217X-RAY DIFFRACTION90
3.4411-3.78740.33761370.30551248X-RAY DIFFRACTION90
3.7874-4.33530.28631310.28211220X-RAY DIFFRACTION90
4.3353-5.46140.28981360.27311250X-RAY DIFFRACTION90
5.4614-59.64910.31491470.31931275X-RAY DIFFRACTION90

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