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- PDB-1bim: CRYSTALLOGRAPHIC STUDIES ON THE BINDING MODES OF P2-P3 BUTANEDIAM... -

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Basic information

Entry
Database: PDB / ID: 1bim
TitleCRYSTALLOGRAPHIC STUDIES ON THE BINDING MODES OF P2-P3 BUTANEDIAMIDE RENIN INHIBITORS
ComponentsRenin
KeywordsHYDROLASE/HYDROLASE INHIBITOR / ASPARTIC PROTEINASE / Aspartyl protease / Cleavage on pair of basic residues / Disease mutation / Disulfide bond / Glycoprotein / Hydrolase / Membrane / Protease / Secreted / Zymogen / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


renin / mesonephros development / juxtaglomerular apparatus development / response to cGMP / renin-angiotensin regulation of aldosterone production / drinking behavior / response to immobilization stress / regulation of MAPK cascade / response to cAMP / amyloid-beta metabolic process ...renin / mesonephros development / juxtaglomerular apparatus development / response to cGMP / renin-angiotensin regulation of aldosterone production / drinking behavior / response to immobilization stress / regulation of MAPK cascade / response to cAMP / amyloid-beta metabolic process / Metabolism of Angiotensinogen to Angiotensins / cell maturation / angiotensin maturation / hormone-mediated signaling pathway / insulin-like growth factor receptor binding / kidney development / regulation of blood pressure / male gonad development / cellular response to xenobiotic stimulus / apical part of cell / peptidase activity / response to lipopolysaccharide / aspartic-type endopeptidase activity / signaling receptor binding / proteolysis / extracellular space / extracellular region / plasma membrane
Similarity search - Function
Renin-like domain / Aspartic peptidase, N-terminal / A1 Propeptide / 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 ...Renin-like domain / Aspartic peptidase, N-terminal / A1 Propeptide / 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 speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / Resolution: 2.8 Å
AuthorsTong, L.
CitationJournal: J.Biol.Chem. / Year: 1995
Title: Crystallographic studies on the binding modes of P2-P3 butanediamide renin inhibitors.
Authors: Tong, L. / Pav, S. / Lamarre, D. / Simoneau, B. / Lavallee, P. / Jung, G.
History
DepositionSep 27, 1995Processing site: BNL
Revision 1.0Jan 29, 1996Provider: 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 1.3Jan 18, 2012Group: Non-polymer description
Revision 1.4Dec 12, 2012Group: Other
Revision 1.5Jul 17, 2019Group: Data collection / Other / Refinement description / Category: pdbx_database_status / software
Item: _pdbx_database_status.process_site / _software.classification
Revision 1.6Aug 14, 2019Group: Data collection / Refinement description / Category: software / Item: _software.classification
Revision 1.7Mar 9, 2022Group: Database references / Derived calculations / Structure summary
Category: database_2 / pdbx_molecule_features / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.8Oct 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: Renin
B: Renin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,2454
Polymers73,8792
Non-polymers1,3662
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)142.900, 142.900, 142.900
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number198
Space group name H-MP213
Atom site foot note1: CIS PROLINE - PRO A 23 / 2: CIS PROLINE - PRO A 111 / 3: CIS PROLINE - PRO A 294 / 4: CIS PROLINE - PRO A 297 / 5: CIS PROLINE - PRO B 23 / 6: CIS PROLINE - PRO B 111 / 7: CIS PROLINE - PRO B 294 / 8: CIS PROLINE - PRO B 297

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Components

#1: Protein Renin / Angiotensinogenase


Mass: 36939.594 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: GLYCOSYLATED / Source: (gene. exp.) Homo sapiens (human) / Description: STABLY TRANSFERRED / Gene: CMV IE-HUMAN PREPRORENIN CDNA, REN / Plasmid: PMNC RETROVIRAL VECTOR / Species (production host): Canis lupus / Gene (production host): CMV IE-HUMAN PREPRORENIN CDNA / Production host: Canis lupus familiaris (dog) / Strain (production host): familiaris / References: UniProt: P00797, renin
#2: Chemical ChemComp-0QB / (2S)-2-[(2-amino-1,3-thiazol-4-yl)methyl]-N~1~-{(1S,2S)-1-(cyclohexylmethyl)-2-hydroxy-2-[(3R)-1,5,5-trimethyl-2-oxopyrrolidin-3-yl]ethyl}-N~4~-[2-(dimethylamino)-2-oxoethyl]-N~4~-[(1S)-1-phenylethyl]butanediamide / P2-P3 butanediamide renin inhibitor (3)


Mass: 682.916 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C36H54N6O5S
Has protein modificationY
Nonpolymer detailsHET GROUPS DMF, PHC, HII, CHA AND IP4 FORM AN INHIBITOR AND REFERRED TO AS INHIBITOR NUMBER 3 IN ...HET GROUPS DMF, PHC, HII, CHA AND IP4 FORM AN INHIBITOR AND REFERRED TO AS INHIBITOR NUMBER 3 IN THE MANUSCRIPT.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.29 Å3/Da / Density % sol: 62.62 %
Crystal
*PLUS
Density % sol: 61 %
Crystal grow
*PLUS
Temperature: 23 ℃ / pH: 4.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
120 mg/mlprotein1drop
250 mMsodium citrate1reservoir
30.6 M1reservoirNaCl
410 %(w/v)PEG33501reservoir

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 2.4 Å / % possible obs: 90 % / Rmerge(I) obs: 0.063

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Processing

Software
NameClassification
X-PLORmodel building
TNTrefinement
X-PLORrefinement
X-PLORphasing
RefinementResolution: 2.8→6 Å / σ(F): 2 /
RfactorNum. reflection
Rwork0.178 -
obs0.178 17435
Refinement stepCycle: LAST / Resolution: 2.8→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5125 0 96 0 5221
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.017
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg2.8
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS

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