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- PDB-1wpx: Crystal structure of carboxypeptidase Y inhibitor complexed with ... -

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Basic information

Entry
Database: PDB / ID: 1wpx
TitleCrystal structure of carboxypeptidase Y inhibitor complexed with the cognate proteinase
Components
  • Carboxypeptidase Y
  • Carboxypeptidase Y inhibitor
KeywordsHYDROLASE / Carboxypeptidase inhibitor / serine proteinase inhibitor / proteinase-inhibitor complex / phosphatidylethanolamine-binding protein / phospholipid
Function / homology
Function and homology information


phytochelatin biosynthetic process / fungal-type vacuole lumen / carboxypeptidase C / serine-type carboxypeptidase activity / regulation of Ras protein signal transduction / peptidase inhibitor activity / fungal-type vacuole / regulation of proteolysis / zymogen activation / fungal-type vacuole membrane ...phytochelatin biosynthetic process / fungal-type vacuole lumen / carboxypeptidase C / serine-type carboxypeptidase activity / regulation of Ras protein signal transduction / peptidase inhibitor activity / fungal-type vacuole / regulation of proteolysis / zymogen activation / fungal-type vacuole membrane / macroautophagy / serine-type endopeptidase inhibitor activity / phospholipid binding / endoplasmic reticulum / extracellular region / cytoplasm
Similarity search - Function
Helix Hairpins - #410 / Propeptide, carboxypeptidase Y / Carboxypeptidase Y pro-peptide / Phosphatidylethanolamine-binding, conserved site / Serine carboxypeptidase, serine active site / Serine carboxypeptidases, serine active site. / Phosphatidylethanolamine-binding protein family signature. / Peptidase S10, serine carboxypeptidase / Serine carboxypeptidases, histidine active site / Serine carboxypeptidase ...Helix Hairpins - #410 / Propeptide, carboxypeptidase Y / Carboxypeptidase Y pro-peptide / Phosphatidylethanolamine-binding, conserved site / Serine carboxypeptidase, serine active site / Serine carboxypeptidases, serine active site. / Phosphatidylethanolamine-binding protein family signature. / Peptidase S10, serine carboxypeptidase / Serine carboxypeptidases, histidine active site / Serine carboxypeptidase / Serine carboxypeptidases, histidine active site. / Phosphatidylethanolamine-binding Protein / PEBP-like / Phosphatidylethanolamine-binding protein / Phosphatidylethanolamine-binding protein / Phosphatidylethanolamine-binding protein, eukaryotic / PEBP-like superfamily / Alpha/Beta hydrolase fold, catalytic domain / Helix Hairpins / Alpha/Beta hydrolase fold / Alpha-Beta Complex / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Carboxypeptidase Y / Carboxypeptidase Y inhibitor
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsMima, J. / Hayashida, M. / Fujii, T. / Narita, Y. / Hayashi, R. / Ueda, M. / Hata, Y.
CitationJournal: J.Mol.Biol. / Year: 2005
Title: Structure of the carboxypeptidase y inhibitor i(c) in complex with the cognate proteinase reveals a novel mode of the proteinase-protein inhibitor interaction
Authors: Mima, J. / Hayashida, M. / Fujii, T. / Narita, Y. / Hayashi, R. / Ueda, M. / Hata, Y.
History
DepositionSep 14, 2004Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 1, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_PDB_caveat / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_validate_chiral / 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_atom_id / _atom_site.auth_comp_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _pdbx_nonpoly_scheme.entity_id / _pdbx_nonpoly_scheme.mon_id / _pdbx_nonpoly_scheme.pdb_mon_id / _struct_asym.entity_id / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_label_comp_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: Carboxypeptidase Y
B: Carboxypeptidase Y inhibitor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,6227
Polymers71,7672
Non-polymers8565
Water91951
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4460 Å2
ΔGint-58 kcal/mol
Surface area23270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.129, 186.590, 65.140
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Carboxypeptidase Y / Carboxypeptidase YSCY


Mass: 47355.363 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P00729, carboxypeptidase C
#2: Protein Carboxypeptidase Y inhibitor / CPY inhibitor / Ic / IC / DKA1 protein / NSP1 protein / TFS1 protein


Mass: 24411.309 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P14306
#3: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 3
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-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 51 / Source method: isolated from a natural source / Formula: H2O

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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: 3.16 Å3/Da / Density % sol: 61 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.7
Details: 0.1M Sodium acetate, 1.95M ammonium sulfate, pH 4.7, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jan 7, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.7→44.99 Å / Num. obs: 28017 / Biso Wilson estimate: 56.6 Å2
Reflection shellResolution: 2.7→2.8 Å

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.7→44.99 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 1566324.26 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.225 2456 8.8 %RANDOM
Rwork0.183 ---
obs0.183 27780 99.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 40.4796 Å2 / ksol: 0.346374 e/Å3
Displacement parametersBiso mean: 38.4 Å2
Baniso -1Baniso -2Baniso -3
1-7.93 Å20 Å20 Å2
2---7.25 Å20 Å2
3----0.68 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.36 Å0.27 Å
Luzzati d res low-5 Å
Luzzati sigma a0.42 Å0.32 Å
Refinement stepCycle: LAST / Resolution: 2.7→44.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4960 0 52 51 5063
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d24
X-RAY DIFFRACTIONc_improper_angle_d0.82
LS refinement shellResolution: 2.7→2.87 Å / Rfactor Rfree error: 0.025 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.33 179 3.9 %
Rwork0.261 4386 -
obs-4386 100 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2CAPPING.PARAMWATER.TOP
X-RAY DIFFRACTION3CARBOHYDRATE.PARAMCARBOHYDRATE.TOP
X-RAY DIFFRACTION4WATER_REP.PARAMCAPPING.TOP
X-RAY DIFFRACTION5ION.PARAMION.TOP

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