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- PDB-3apr: BINDING OF A REDUCED PEPTIDE INHIBITOR TO THE ASPARTIC PROTEINASE... -

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Basic information

Entry
Database: PDB / ID: 3apr
TitleBINDING OF A REDUCED PEPTIDE INHIBITOR TO THE ASPARTIC PROTEINASE FROM RHIZOPUS CHINENSIS. IMPLICATIONS FOR A MECHANISM OF ACTION
Components
  • REDUCED PEPTIDE INHIBITOR
  • RHIZOPUSPEPSIN
KeywordsHYDROLASE/HYDROLASE INHIBITOR / HYDROLASE / ASPARTIC PROTEINASE / HYDROLASE-HYDROLASE INHIBITOR COMPLEX
Function / homology
Function and homology information


rhizopuspepsin / aspartic-type endopeptidase activity / proteolysis
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
N-[(2R)-3-phenyl-2-{[L-prolyl-L-phenylalanyl-3-(1H-imidazol-3-ium-4-yl)-L-alanyl]amino}propyl]-L-phenylalanyl-L-valylty rosine / Rhizopuspepsin
Similarity search - Component
Biological speciesRhizopus microsporus var. chinensis (fungus)
MethodX-RAY DIFFRACTION / Resolution: 1.8 Å
AuthorsSuguna, K. / Davies, D.R.
Citation
Journal: Proc.Natl.Acad.Sci.USA / Year: 1987
Title: Binding of a reduced peptide inhibitor to the aspartic proteinase from Rhizopus chinensis: implications for a mechanism of action.
Authors: Suguna, K. / Padlan, E.A. / Smith, C.W. / Carlson, W.D. / Davies, D.R.
#1: Journal: J.Mol.Biol. / Year: 1987
Title: Structure and Refinement at 1.8 Angstroms Resolution of the Aspartic Proteinase from Rhizopus Chinensis
Authors: Suguna, K. / Bott, R.R. / Padlan, E.A. / Subramanian, E. / Sheriff, S. / Cohen, G.H. / Davies, D.R.
#2: Journal: Biochemistry / Year: 1982
Title: Three-Dimensional Structure of the Complex of the Rhizopus Chinensis Carboxyl Proteinase and Pepstatin at 2.5 Angstroms Resolution
Authors: Bott, R.R. / Subramanian, E. / Davies, D.R.
#3: Journal: Adv.Exp.Med.Biol. / Year: 1977
Title: The Crystal Structure of an Acid Protease from Rhizopus Chinensis at 2.5 Angstroms Resolution
Authors: Subramanian, E. / Liu, M. / Swan, I.D.A. / Davies, D.R.
#4: Journal: Proc.Natl.Acad.Sci.USA / Year: 1977
Title: Homology Among Acid Proteases. Comparison of Crystal Structures at 3 Angstroms Resolution of Acid Proteases from Rhizopus Chinensis and Endothia Parasitica
Authors: Subramanian, E. / Swan, I.D.A. / Liu, M. / Davies, D.R. / Jenkins, J.A. / Tickle, I.J. / Blundell, T.L.
History
DepositionJun 22, 1987Processing site: BNL
Revision 1.0Jan 16, 1988Provider: repository / Type: Initial release
Revision 1.1Mar 3, 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 12, 2012Group: Other
Revision 1.4Nov 29, 2017Group: Derived calculations / Other
Category: pdbx_database_status / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_validate_main_chain_plane / pdbx_validate_peptide_omega / pdbx_validate_rmsd_angle / struct_conn / struct_ref_seq_dif
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 2.1Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification
Remark 700SHEET THERE ARE SEVERAL BIFURCATED SHEETS IN THIS STRUCTURE. THESE ARE REPRESENTED BY TWO SHEETS ...SHEET THERE ARE SEVERAL BIFURCATED SHEETS IN THIS STRUCTURE. THESE ARE REPRESENTED BY TWO SHEETS WHICH HAVE ONE OR MORE IDENTICAL STRANDS. SHEETS *S2A* AND *S2B* REPRESENT ONE BIFURCATED SHEET. SHEETS *S3A* AND *S3B* REPRESENT ONE BIFURCATED SHEET. SHEETS *S4A* AND *S4B* REPRESENT ONE BIFURCATED SHEET.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
E: RHIZOPUSPEPSIN
I: REDUCED PEPTIDE INHIBITOR


Theoretical massNumber of molelcules
Total (without water)35,1502
Polymers35,1502
Non-polymers00
Water6,197344
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1390 Å2
ΔGint-8 kcal/mol
Surface area12930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.370, 60.610, 106.770
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Atom site foot note1: RESIDUES PRO E 26 AND PRO E 316 ARE CIS PROLINES. / 2: SEE REMARK 5. / 3: SEE REMARK 6.

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Components

#1: Protein RHIZOPUSPEPSIN


Mass: 34068.629 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhizopus microsporus var. chinensis (fungus)
References: UniProt: P06026, EC: 3.4.23.6
#2: Protein/peptide REDUCED PEPTIDE INHIBITOR


Type: Peptide-like / Class: Inhibitor / Mass: 1081.266 Da / Num. of mol.: 1 / Source method: obtained synthetically
References: N-[(2R)-3-phenyl-2-{[L-prolyl-L-phenylalanyl-3-(1H-imidazol-3-ium-4-yl)-L-alanyl]amino}propyl]-L-phenylalanyl-L-valylty rosine
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 344 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Nonpolymer detailsTHERE IS A REDUCED PEPTIDE BOND BETWEEN PHE I 5 AND PHE I 6. IN THIS ENTRY IT IS IDENTIFIED AS PUK ...THERE IS A REDUCED PEPTIDE BOND BETWEEN PHE I 5 AND PHE I 6. IN THIS ENTRY IT IS IDENTIFIED AS PUK I 5 AND THE ATOMS ARE PRESENTED ON *HETATM* RECORDS.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.78 Å3/Da / Density % sol: 55.74 %
Crystal grow
*PLUS
pH: 6 / Method: unknown / Details: referred to J.Mol.Biol. 196.877-900 1987
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
120 mMcalcium acetate11
250 mg/mlprotein11

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 1.8 Å / Num. obs: 36590 / Num. measured all: 118370 / Rmerge(I) obs: 0.045

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Processing

SoftwareName: PROLSQ / Classification: refinement
RefinementRfactor obs: 0.147 / Highest resolution: 1.8 Å
Details: THERE IS DISORDER AT SER E 116, ARG E 151, ARG E 192, AND SER E 211.
Refine analyzeLuzzati coordinate error obs: 0.16 Å
Refinement stepCycle: LAST / Highest resolution: 1.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2460 0 0 344 2804
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.009
X-RAY DIFFRACTIONp_angle_d0.034
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
Refinement
*PLUS
Highest resolution: 1.8 Å / Rfactor obs: 0.147
Solvent computation
*PLUS
Displacement parameters
*PLUS

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