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- PDB-4apr: STRUCTURES OF COMPLEXES OF RHIZOPUSPEPSIN WITH PEPSTATIN AND OTHE... -

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Basic information

Entry
Database: PDB / ID: 4apr
TitleSTRUCTURES OF COMPLEXES OF RHIZOPUSPEPSIN WITH PEPSTATIN AND OTHER STATINE-CONTAINING INHIBITORS
Components
  • PEPSTATIN-LIKE RENIN INHIBITOR
  • RHIZOPUSPEPSIN
KeywordsHYDROLASE/HYDROLASE INHIBITOR / ACID 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
Biological speciesRhizopus chinensis (fungus)
MethodX-RAY DIFFRACTION / Resolution: 2.5 Å
AuthorsSuguna, K. / Davies, D.R.
Citation
Journal: Proteins / Year: 1992
Title: Structures of complexes of rhizopuspepsin with pepstatin and other statine-containing inhibitors.
Authors: Suguna, K. / Padlan, E.A. / Bott, R. / Boger, J. / Parris, K.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
DepositionAug 3, 1989Processing site: BNL
Revision 1.0Apr 15, 1991Provider: 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 1.3May 23, 2012Group: Source and taxonomy
Revision 1.4Nov 29, 2017Group: Derived calculations / Other
Category: pdbx_database_status / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site
Revision 1.5Oct 23, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
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: PEPSTATIN-LIKE RENIN INHIBITOR


Theoretical massNumber of molelcules
Total (without water)35,1092
Polymers35,1092
Non-polymers00
Water5,621312
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1260 Å2
ΔGint-10 kcal/mol
Surface area13110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.390, 60.610, 106.900
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.

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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 chinensis (fungus) / References: UniProt: P06026, EC: 3.4.23.6
#2: Protein/peptide PEPSTATIN-LIKE RENIN INHIBITOR


Mass: 1040.255 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 312 / 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: 2.79 Å3/Da / Density % sol: 55.84 %
Crystal grow
*PLUS
pH: 6 / Method: other / Details: grown in the cold from a filtered
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110 mg/mlenzyme solution11
250 mMcacodylate11
320 mMcalcium acetate11

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 2.5 Å / Num. all: 18623 / Num. obs: 13024 / Rmerge(I) obs: 0.085

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Processing

SoftwareName: PROLSQ / Classification: refinement
RefinementResolution: 2.5→7 Å / σ(F): 0
Details: THERE IS DISORDER AT SER E 116, ARG E 151, ARG E 192 AND SER E 211.
RfactorNum. reflection
obs0.154 12274
Refinement stepCycle: LAST / Resolution: 2.5→7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2450 0 0 312 2762
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0110.015
X-RAY DIFFRACTIONp_angle_d0.040.03
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0480.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it0.841
X-RAY DIFFRACTIONp_mcangle_it1.4651.5
X-RAY DIFFRACTIONp_scbond_it0.7791
X-RAY DIFFRACTIONp_scangle_it1.3571.5
X-RAY DIFFRACTIONp_plane_restr0.0090.015
X-RAY DIFFRACTIONp_chiral_restr0.110.1
X-RAY DIFFRACTIONp_singtor_nbd0.160.2
X-RAY DIFFRACTIONp_multtor_nbd0.1710.2
X-RAY DIFFRACTIONp_xhyhbond_nbd0.1830.2
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor1.72
X-RAY DIFFRACTIONp_staggered_tor15.712
X-RAY DIFFRACTIONp_orthonormal_tor27.720
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Refinement
*PLUS
Highest resolution: 2.5 Å / Lowest resolution: 7 Å / Num. reflection obs: 12274 / σ(F): 1 / Rfactor obs: 0.154
Solvent computation
*PLUS
Displacement parameters
*PLUS

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