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- PDB-5dzu: Structure of potato cathepsin D inhibitor -

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Basic information

Entry
Database: PDB / ID: 5dzu
TitleStructure of potato cathepsin D inhibitor
ComponentsAspartic protease inhibitor 11
KeywordsHYDROLASE INHIBITOR / Kunitz-type protease inhibitor
Function / homology
Function and homology information


aspartic-type endopeptidase inhibitor activity / vacuole / serine-type endopeptidase inhibitor activity
Similarity search - Function
Soybean trypsin inhibitor (Kunitz) protease inhibitors family signature. / Proteinase inhibitor I3, Kunitz legume / Trypsin and protease inhibitor / Soybean trypsin inhibitor (Kunitz) family of protease inhibitors / Kunitz inhibitor STI-like superfamily / Trefoil (Acidic Fibroblast Growth Factor, subunit A) - #50 / Trefoil (Acidic Fibroblast Growth Factor, subunit A) / Trefoil / Mainly Beta
Similarity search - Domain/homology
Aspartic protease inhibitor 11
Similarity search - Component
Biological speciesSolanum tuberosum (potato)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.12 Å
AuthorsGuo, J. / Erskine, P. / Coker, A.R. / Wood, S.P. / Cooper, J.B.
CitationJournal: J.Struct.Biol. / Year: 2015
Title: Structure of a Kunitz-type potato cathepsin D inhibitor.
Authors: Guo, J. / Erskine, P.T. / Coker, A.R. / Wood, S.P. / Cooper, J.B.
History
DepositionSep 26, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Oct 21, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 18, 2015Group: Database references
Revision 1.2Nov 25, 2015Group: Database references
Revision 1.3Apr 25, 2018Group: Data collection / Category: reflns_shell / Item: _reflns_shell.Rmerge_I_obs
Revision 1.4Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.5Jan 10, 2024Group: 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 1.6Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Aspartic protease inhibitor 11
B: Aspartic protease inhibitor 11
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,6816
Polymers41,2132
Non-polymers4674
Water2,216123
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1800 Å2
ΔGint6 kcal/mol
Surface area18470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.458, 124.769, 37.876
Angle α, β, γ (deg.)90.00, 95.14, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Aspartic protease inhibitor 11 / Cathepsin D inhibitor PDI


Mass: 20606.568 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Solanum tuberosum (potato) / References: UniProt: P16348
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C3H8O3
#3: 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: isolated from a genetically manipulated source
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
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 123 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.22 Å3/Da / Density % sol: 44.62 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / Details: 2.0 M NaCl, 10% PEG 6000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.917 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: May 17, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.917 Å / Relative weight: 1
ReflectionResolution: 2.11→27.9 Å / Num. all: 19943 / Num. obs: 19145 / % possible obs: 96 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.073 / Net I/σ(I): 8.3
Reflection shellResolution: 2.11→2.17 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.969 / Mean I/σ(I) obs: 0.8 / % possible all: 70.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0131refinement
XDS31.10.2011data reduction
Aimless0.5.7data scaling
MOLREP11.3.02phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3TC2

3tc2


Resolution: 2.12→64.38 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.923 / SU B: 9.881 / SU ML: 0.238 / Cross valid method: THROUGHOUT / ESU R: 0.283 / ESU R Free: 0.237 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26979 952 5 %RANDOM
Rwork0.19148 ---
obs0.19544 18191 96.4 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 48.877 Å2
Baniso -1Baniso -2Baniso -3
1-1.56 Å20 Å21.19 Å2
2--0.86 Å2-0 Å2
3----2.59 Å2
Refinement stepCycle: LAST / Resolution: 2.12→64.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2794 0 30 123 2947
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.022891
X-RAY DIFFRACTIONr_bond_other_d0.0020.022762
X-RAY DIFFRACTIONr_angle_refined_deg1.6291.9913931
X-RAY DIFFRACTIONr_angle_other_deg0.9973.0026360
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.6435360
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.17724.426122
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.8515456
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.9741515
X-RAY DIFFRACTIONr_chiral_restr0.090.2441
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0213282
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02649
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.5584.7261448
X-RAY DIFFRACTIONr_mcbond_other3.5594.7271447
X-RAY DIFFRACTIONr_mcangle_it5.5997.0721805
X-RAY DIFFRACTIONr_mcangle_other5.5977.0711806
X-RAY DIFFRACTIONr_scbond_it3.515.1071441
X-RAY DIFFRACTIONr_scbond_other3.5095.111442
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.6017.5312126
X-RAY DIFFRACTIONr_long_range_B_refined8.40437.8013112
X-RAY DIFFRACTIONr_long_range_B_other8.35737.8073098
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.117→2.172 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.347 45 -
Rwork0.37 1065 -
obs--76.76 %

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