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- PDB-1apu: Crystallographic analysis of a pepstatin analogue binding to the ... -

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Basic information

Entry
Database: PDB / ID: 1apu
TitleCrystallographic analysis of a pepstatin analogue binding to the aspartyl proteinase penicillopepsin at 1.8 angstroms resolution
Components
  • PEPSTATIN ANALOGUE ISOVALERYL-VAL-VAL-STA-O-ET
  • PROTEIN (PENICILLOPEPSIN)
KeywordsHYDROLASE/HYDROLASE INHIBITOR / ACID PROTEINASE / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


penicillopepsin / aspartic-type endopeptidase activity / proteolysis / extracellular region
Similarity search - Function
Aspergillopepsin-like catalytic domain / 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 ...Aspergillopepsin-like catalytic domain / 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
PEPSTATIN ANALOGUE ISOVALERYL-VAL-VAL-STA-O-ET / alpha-D-mannopyranose / Penicillopepsin-1
Similarity search - Component
Biological speciesPenicillium janthinellum (fungus)
MethodX-RAY DIFFRACTION / Resolution: 1.8 Å
AuthorsSielecki, A.R. / James, M.N.G.
Citation
Journal: Biochemistry / Year: 1992
Title: Crystallographic Analysis of Transition State Mimics Bound to Penicillopepsin: Difluorostatine-and Difluorostatone-Containing Peptides
Authors: James, M.N.G. / Sielecki, A.R. / Moult, J.
#1: Journal: Peptides: Structure and Function, Proceedings of the of the Eighth American Peptide Symposium
Year: 1983
Title: Crystallographic Analysis of a Pepstatin Analogue Binding to the Aspartyl Proteinase Penicillopepsin at 1.8 Angstroms Resolution
Authors: James, M.N.G. / Sielecki, A.R. / Hayakawa, K. / Gelb, M.H.
#2: Journal: Biological Macromolecules and Assemblies / Year: 1987
Title: Aspartic Proteinases and Their Catalytic Pathway
Authors: James, M.N.G. / Sielecki, A.R.
#3: Journal: Biochemistry / Year: 1985
Title: Stereochemical Analysis of Peptide Bond Hydrolysis Catalyzed by the Aspartic Proteinase Penicillopepsin
Authors: James, M.N.G. / Sielecki, A.R.
#4: Journal: Aspartic Proteinases and Their Inhibitors / Year: 1985
Title: X-Ray Diffraction Studies on Penicillopepsin and its Complexes: The Hydrolytic Mechanism
Authors: James, M.N.G. / Sielecki, A.R. / Hofmann, T.
#5: Journal: Biochemistry / Year: 1984
Title: Effect of Ph on the Activities of Penicillopepsin and Rhizopus Pepsin and a Proposal for the Productive Substrate Binding Mode in Penicillopepsin
Authors: Hofmann, T. / Hodges, R.S. / James, M.N.G.
#6: Journal: J.Mol.Biol. / Year: 1983
Title: Structure and Refinement of Penicillopepsin at 1.8 Angstroms Resolution
Authors: James, M.N.G. / Sielecki, A.R.
#7: Journal: Proc.Natl.Acad.Sci.USA / Year: 1982
Title: Conformational Flexibility in the Active Sites of Aspartyl Proteinases Revealed by a Pepstatin Fragment Binding to Penicillopepsin
Authors: James, M.N.G. / Sielecki, A. / Salituro, F. / Rich, D.H. / Hofmann, T.
History
DepositionDec 16, 1991Processing site: BNL
Revision 1.0Jan 31, 1994Provider: repository / Type: Initial release
Revision 1.1Mar 24, 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 1.3Jun 4, 2014Group: Structure summary
Revision 1.4Jul 29, 2020Group: Data collection / Derived calculations ...Data collection / Derived calculations / Other / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_database_status / 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_database_status.process_site / _pdbx_entity_nonpoly.name / _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_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 1.5Oct 16, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
E: PROTEIN (PENICILLOPEPSIN)
I: PEPSTATIN ANALOGUE ISOVALERYL-VAL-VAL-STA-O-ET
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,1353
Polymers33,9542
Non-polymers1801
Water5,675315
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1230 Å2
ΔGint-4 kcal/mol
Surface area12480 Å2
MethodPISA
2
E: PROTEIN (PENICILLOPEPSIN)
I: PEPSTATIN ANALOGUE ISOVALERYL-VAL-VAL-STA-O-ET
hetero molecules

E: PROTEIN (PENICILLOPEPSIN)
I: PEPSTATIN ANALOGUE ISOVALERYL-VAL-VAL-STA-O-ET
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,2696
Polymers67,9094
Non-polymers3602
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area4350 Å2
ΔGint-4 kcal/mol
Surface area23070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.240, 46.500, 65.650
Angle α, β, γ (deg.)90.00, 115.34, 90.00
Int Tables number5
Space group name H-MC121
Atom site foot note1: RESIDUES PRO E 134 AND PRO E 315 ARE CIS PROLINES.
2: THE REGION FROM SER E 277 TO SER E 281 IS POORLY ORDERED.
Components on special symmetry positions
IDModelComponents
11E-577-

HOH

21E-720-

HOH

31E-754-

HOH

41E-793-

HOH

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Components

#1: Protein PROTEIN (PENICILLOPEPSIN) / Peptidase A


Mass: 33468.809 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Penicillium janthinellum (fungus) / References: UniProt: P00798, penicillopepsin
#2: Protein/peptide PEPSTATIN ANALOGUE ISOVALERYL-VAL-VAL-STA-O-ET


Type: Oligopeptide / Class: Enzyme inhibitor / Mass: 485.657 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
References: PEPSTATIN ANALOGUE ISOVALERYL-VAL-VAL-STA-O-ET
#3: Sugar ChemComp-MAN / alpha-D-mannopyranose / alpha-D-mannose / D-mannose / mannose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DManpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-mannopyranoseCOMMON NAMEGMML 1.0
a-D-ManpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
ManSNFG CARBOHYDRATE SYMBOLGMML 1.0
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 315 / 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: 1.98 Å3/Da / Density % sol: 37.74 %

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1

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Processing

SoftwareName: PROLSQ / Classification: refinement
RefinementResolution: 1.8→8 Å / σ(I): 1 /
RfactorNum. reflection
obs0.131 21197
Refinement stepCycle: LAST / Resolution: 1.8→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2400 0 11 315 2726
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.015
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it
X-RAY DIFFRACTIONp_mcangle_it
X-RAY DIFFRACTIONp_scbond_it
X-RAY DIFFRACTIONp_scangle_it
X-RAY DIFFRACTIONp_plane_restr
X-RAY DIFFRACTIONp_chiral_restr
X-RAY DIFFRACTIONp_singtor_nbd
X-RAY DIFFRACTIONp_multtor_nbd
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor
X-RAY DIFFRACTIONp_staggered_tor
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor

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