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- PDB-1dp5: THE STRUCTURE OF PROTEINASE A COMPLEXED WITH A IA3 MUTANT INHIBITOR -

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Basic information

Entry
Database: PDB / ID: 1dp5
TitleTHE STRUCTURE OF PROTEINASE A COMPLEXED WITH A IA3 MUTANT INHIBITOR
Components
  • PROTEINASE A
  • PROTEINASE INHIBITOR IA3
KeywordsHYDROLASE/HYDROLASE INHIBITOR / Proteinase A / MMM / IA3 mutant / HYDROLASE-HYDROLASE INHIBITOR COMPLEX
Function / homology
Function and homology information


saccharopepsin / protein catabolic process in the vacuole / microautophagy / cytoplasm to vacuole targeting by the Cvt pathway / negative regulation of endopeptidase activity / oligosaccharide binding / aspartic-type endopeptidase inhibitor activity / pexophagy / fungal-type vacuole / vacuole ...saccharopepsin / protein catabolic process in the vacuole / microautophagy / cytoplasm to vacuole targeting by the Cvt pathway / negative regulation of endopeptidase activity / oligosaccharide binding / aspartic-type endopeptidase inhibitor activity / pexophagy / fungal-type vacuole / vacuole / endopeptidase inhibitor activity / proteolysis involved in protein catabolic process / macroautophagy / autophagy / disordered domain specific binding / peptidase activity / protease binding / aspartic-type endopeptidase activity / endoplasmic reticulum / protein-containing complex / mitochondrion / nucleus / cytoplasm
Similarity search - Function
Protease A inhibitor IA3 domain superfamily / Protease A inhibitor IA3 / Saccharopepsin inhibitor I34 / Saccharopepsin / Eukaryotic aspartyl protease / Aspartic peptidase A1 family / Peptidase family A1 domain / Peptidase family A1 domain profile. / Cathepsin D, subunit A; domain 1 / Acid Proteases ...Protease A inhibitor IA3 domain superfamily / Protease A inhibitor IA3 / Saccharopepsin inhibitor I34 / Saccharopepsin / Eukaryotic aspartyl protease / Aspartic peptidase A1 family / Peptidase family A1 domain / Peptidase family A1 domain profile. / Cathepsin D, subunit A; domain 1 / Acid Proteases / Aspartic peptidase, active site / Eukaryotic and viral aspartyl proteases active site. / Aspartic peptidase domain superfamily / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Protease A inhibitor 3 / Saccharopepsin
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.2 Å
AuthorsLi, M. / Phylip, H.L. / Lees, W.E. / Winther, J.R. / Dunn, B.M. / Wlodawer, A. / Kay, J. / Guschina, A.
Citation
Journal: Nat.Struct.Biol. / Year: 2000
Title: The aspartic proteinase from Saccharomyces cerevisiae folds its own inhibitor into a helix.
Authors: Li, M. / Phylip, L.H. / Lees, W.E. / Winther, J.R. / Dunn, B.M. / Wlodawer, A. / Kay, J. / Gustchina, A.
#1: Journal: J.Mol.Biol. / Year: 1997
Title: The Three-dimensional Structure at 2.4 A Resolution of Glycosylated Proteinase A from the Lysosome-like Vacuole of Saccharomyces Cerevisiae.
Authors: Aguilar, C.F. / Cronin, N.B. / Badasso, M. / Dreyer, T. / Newman, M.P. / Cooper, J.B. / Hoover, D.J. / Wood, S.P. / Johnson, M.S. / Blundell, T.L.
History
DepositionDec 23, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 3, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 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 / 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_unobs_or_zero_occ_atoms / 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 / _struct_conn.details / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _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
Revision 2.1Nov 3, 2021Group: Advisory / Database references / Structure summary
Category: chem_comp / database_2 ...chem_comp / database_2 / pdbx_unobs_or_zero_occ_atoms / struct_ref_seq_dif
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 2.2Oct 16, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PROTEINASE A
B: PROTEINASE INHIBITOR IA3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,0603
Polymers43,5012
Non-polymers1,5591
Water7,044391
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5430 Å2
ΔGint9 kcal/mol
Surface area14580 Å2
MethodPISA
2
A: PROTEINASE A
B: PROTEINASE INHIBITOR IA3
hetero molecules

A: PROTEINASE A
B: PROTEINASE INHIBITOR IA3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,1216
Polymers87,0024
Non-polymers3,1192
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation11_556-x+y,y,-z+11
Buried area11440 Å2
ΔGint24 kcal/mol
Surface area28580 Å2
MethodPISA
3
A: PROTEINASE A
B: PROTEINASE INHIBITOR IA3
hetero molecules

A: PROTEINASE A
B: PROTEINASE INHIBITOR IA3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,1216
Polymers87,0024
Non-polymers3,1192
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_675x-y+1,-y+2,-z1
Buried area13440 Å2
ΔGint2 kcal/mol
Surface area26580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)192.660, 192.660, 52.080
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number180
Space group name H-MP6222

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Components

#1: Protein PROTEINASE A / ASPARTATE PROTEASE


Mass: 35774.551 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P07267, saccharopepsin
#2: Protein PROTEINASE INHIBITOR IA3 / IA3


Mass: 7726.512 Da / Num. of mol.: 1 / Mutation: K31M, K32M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Production host: Escherichia coli (E. coli) / References: UniProt: P01094
#3: Polysaccharide beta-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-[alpha-D-mannopyranose-(1-6)]alpha-D- ...beta-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-3)-[beta-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1559.386 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-2DManpa1-2[DManpa1-6]DManpa1-3[DManpb1-6DManpa1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,9,8/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3-2-3-3-2/a4-b1_b4-c1_c3-d1_c6-h1_d2-e1_d6-g1_e2-f1_h6-i1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{[(2+1)][a-D-Manp]{[(2+1)][b-D-Manp]{}}[(6+1)][a-D-Manp]{}}[(6+1)][a-D-Manp]{[(6+1)][b-D-Manp]{}}}}}}LINUCSPDB-CARE
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 391 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHE RESIDUE NUMBERS FOR CHAIN A FOLLOW THE RESIDUE NUMBERS IN PDB ENTRY 2JXR. THE SEQUENCE FOR ...THE RESIDUE NUMBERS FOR CHAIN A FOLLOW THE RESIDUE NUMBERS IN PDB ENTRY 2JXR. THE SEQUENCE FOR CHAIN B IS THE FULL LENGTH SEQUENCE.

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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: 3.21 Å3/Da / Density % sol: 61.63 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: PEG 1500, Ammounia Sulfate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 298.K
Crystal grow
*PLUS
pH: 6.6
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
15 mg/mlprotein1drop
228 %PEG15001reservoir
30.2 Mammonium sulfate1reservoir
40.1 MMES1reservoir
520 mMMES1drop

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X9B / Wavelength: 1.54
DetectorType: ADSC QUANTUM / Detector: CCD / Date: Jan 1, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.2→20 Å / Num. all: 29595 / Num. obs: 28115 / % possible obs: 95 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.6 % / Rmerge(I) obs: 0.069 / Net I/σ(I): 16
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.332 / Num. unique all: 2881 / % possible all: 99.6
Reflection
*PLUS
% possible obs: 95.6 % / Redundancy: 5.8 %
Reflection shell
*PLUS
% possible obs: 99.6 % / Mean I/σ(I) obs: 6

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNSrefinement
RefinementResolution: 2.2→30 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber / Details: Residues 33-68 are disordered.
RfactorNum. reflection% reflectionSelection details
Rfree0.235 2615 -random
Rwork0.188 ---
all-26332 --
obs-26332 90 %-
Refinement stepCycle: LAST / Resolution: 2.2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2770 0 105 391 3266
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.011
X-RAY DIFFRACTIONc_angle_deg1.65
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.2 Å / Lowest resolution: 30 Å / σ(F): 0 / Rfactor obs: 0.1883
Solvent computation
*PLUS
Displacement parameters
*PLUS

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