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- PDB-1fq5: X-ray structure of a cyclic statine inhibitor PD-129,541 bound to... -

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Basic information

Entry
Database: PDB / ID: 1fq5
TitleX-ray structure of a cyclic statine inhibitor PD-129,541 bound to yeast proteinase A
ComponentsSACCHAROPEPSIN
KeywordsHYDROLASE/HYDROLASE INHIBITOR / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


saccharopepsin / microautophagy / cytoplasm to vacuole targeting by the Cvt pathway / oligosaccharide binding / pexophagy / fungal-type vacuole / proteolysis involved in protein catabolic process / macroautophagy / autophagy / disordered domain specific binding ...saccharopepsin / microautophagy / cytoplasm to vacuole targeting by the Cvt pathway / oligosaccharide binding / pexophagy / fungal-type vacuole / proteolysis involved in protein catabolic process / macroautophagy / autophagy / disordered domain specific binding / peptidase activity / aspartic-type endopeptidase activity / endoplasmic reticulum / protein-containing complex / mitochondrion
Similarity search - Function
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 ...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
Chem-0GM / Saccharopepsin
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.4 Å
AuthorsCronin, N.B. / Badasso, M.O. / Tickle, I.J. / Dreyer, T. / Hoover, D.J. / Rosati, R.L. / Humblet, C.C. / Lunney, E.A. / Cooper, J.B.
Citation
Journal: J.Mol.Biol. / Year: 2000
Title: X-ray structures of five renin inhibitors bound to saccharopepsin: exploration of active-site specificity.
Authors: Cronin, N.B. / Badasso, M.O. / J Tickle, I. / Dreyer, T. / Hoover, D.J. / Rosati, R.L. / Humblet, C.C. / Lunney, E.A. / Cooper, J.B.
#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
DepositionSep 3, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 20, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Non-polymer description / Structure summary / Version format compliance
Revision 1.3Dec 14, 2016Group: Structure summary
Revision 1.4Oct 4, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_PDB_caveat / 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_validate_chiral / pdbx_validate_close_contact / struct_asym / struct_conn / struct_ref_seq_dif / 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.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _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 / _struct_ref_seq_dif.details
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: SACCHAROPEPSIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,7474
Polymers35,7751
Non-polymers1,9723
Water1,892105
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)87.300, 87.300, 110.700
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein SACCHAROPEPSIN / ASPARTATE PROTEASE / PROTEINASE A


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: Polysaccharide beta-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-4)-2-acetamido-2- ...beta-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 910.823 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-2DManpa1-3DManpa1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,5,4/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1a_1-5][a1122h-1b_1-5]/1-1-2-2-3/a4-b1_b4-c1_c3-d1_d2-e1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Altp]{[(3+1)][b-D-Manp]{[(2+1)][b-D-Manp]{}}}}}}LINUCSPDB-CARE
#3: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose


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-0GM / N-[(5S,9S,10S,13S)-9-hydroxy-5,10-bis(2-methylpropyl)-4,7,12,16-tetraoxo-3,6,11,17-tetraazabicyclo[17.3.1]tricosa-1(23),19,21-trien-13-yl]-3-(naphthalen-1-yl)-2-(naphthalen-1-ylmethyl)propanamide / CP-129,541


Type: peptide-like / Mass: 840.060 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C51H61N5O6
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 105 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsCYCLIC PEPTIDO-MIMETIC STATIN INHIBITOR PD-129,541 WITH KI IN NANOMOLAR RANGE. THE AUTHORS CALL THE ...CYCLIC PEPTIDO-MIMETIC STATIN INHIBITOR PD-129,541 WITH KI IN NANOMOLAR RANGE. THE AUTHORS CALL THE INHIBITOR CYCLIC STATINE INHIBITOR PD-129,541, BNMA(BIS-[(1-NAPHTHYL)METHYL]ACETIC ACID)-GLU-STATINE-LEU-AMPMA(META-DI(AMINOMETHYL)BENZENE)

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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: 3.4 Å3/Da / Density % sol: 63.85 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: PEG 6000, Sodium Acetate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal
*PLUS
Density % sol: 56 %
Crystal grow
*PLUS
Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
110-25 %(w/v)PEG60001reservoir
20.01 Msodium acetate1reservoirpH5.5
310 mg/mlprotein1drop

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX9.5 / Wavelength: 1.01
DetectorType: MARRESEARCH / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.01 Å / Relative weight: 1
ReflectionResolution: 2.4→12.9 Å / Num. all: 25823 / Num. obs: 17302 / % possible obs: 89.6 % / Observed criterion σ(I): 3 / Redundancy: 2.7 % / Rmerge(I) obs: 0.07
Reflection
*PLUS
Num. measured all: 50021 / Rmerge(I) obs: 0.071
Reflection shell
*PLUS
% possible obs: 81.2 % / Rmerge(I) obs: 0.641

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
ROTAVATAdata reduction
AMoREphasing
RESTRAINrefinement
CCP4(AGROVATAdata scaling
ROTAVATAdata scaling
RefinementResolution: 2.4→12.9 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.28 1384 -random
all0.2 17302 --
obs0.2 17302 100 %-
Refinement stepCycle: LAST / Resolution: 2.4→12.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2528 0 137 105 2770
Software
*PLUS
Name: RESTRAIN / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.4 Å / Lowest resolution: 12.9 Å / Num. reflection all: 0 / σ(F): 0 / Rfactor obs: 0.2 / Rfactor Rfree: 0.28 / Rfactor Rwork: 0.2
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.016
X-RAY DIFFRACTIONx_angle_d0.04
X-RAY DIFFRACTIONx_chiral_restr0.02

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