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- PDB-2v13: Crystal Structure of Renin with Inhibitor 7 -

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Basic information

Entry
Database: PDB / ID: 2v13
TitleCrystal Structure of Renin with Inhibitor 7
ComponentsRENIN
KeywordsHYDROLASE / GLYCOPROTEIN / INHIBITOR-COMPLEX / ASPARTYL PROTEASE / ZYMOGEN / PROTEASE / POLYMORPHISM / ALTERNATIVE SPLICING / HYDROLASE(ACID PROTEINASE) / CLEAVAGE ON PAIR OF BASIC RESIDUES
Function / homology
Function and homology information


renin / juxtaglomerular apparatus development / mesonephros development / response to cGMP / response to immobilization stress / regulation of MAPK cascade / response to cAMP / Metabolism of Angiotensinogen to Angiotensins / kidney development / angiotensin maturation ...renin / juxtaglomerular apparatus development / mesonephros development / response to cGMP / response to immobilization stress / regulation of MAPK cascade / response to cAMP / Metabolism of Angiotensinogen to Angiotensins / kidney development / angiotensin maturation / insulin-like growth factor receptor binding / male gonad development / cellular response to xenobiotic stimulus / regulation of blood pressure / apical part of cell / peptidase activity / response to lipopolysaccharide / aspartic-type endopeptidase activity / signaling receptor binding / proteolysis / : / 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 / OTHER / Resolution: 2.8 Å
AuthorsRahuel, J. / Rasetti, V. / Maibaum, J. / Rueger, H. / Goschke, R. / Cohen, N.C. / Stutz, S. / Cumin, F. / Fuhrer, W. / Wood, J.M. / Grutter, M.G.
Citation
Journal: Chem.Biol. / Year: 2000
Title: Structure-Based Drug Design: The Discovery of Novel Nonpeptide Orally Active Inhibitors of Human Renin
Authors: Rahuel, J. / Rasetti, V. / Maibaum, J. / Rueger, H. / Goschke, R. / Cohen, N.C. / Stutz, S. / Cumin, F. / Fuhrer, W. / Wood, J.M. / Grutter, M.G.
#1: Journal: J.Struct.Biol. / Year: 1991
Title: The Crystal Structures of Recombinant Glycosylated Human Renin Alone and in Complex with a Transition State Analog Inhibitor.
Authors: Rahuel, J. / Priestle, J.P. / Grutter, M.G.
History
DepositionMay 21, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 8, 2008Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jun 28, 2017Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.4Jul 12, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.5Apr 3, 2019Group: Data collection / Source and taxonomy / Category: entity_src_gen / Item: _entity_src_gen.pdbx_host_org_cell_line
Revision 1.6Oct 9, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RENIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,7332
Polymers37,2671
Non-polymers4661
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)98.400, 98.400, 95.600
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein RENIN / ANGIOTENSINOGENASE


Mass: 37267.008 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Cell line (production host): CHO / Production host: CRICETULUS GRISEUS (Chinese hamster) / References: UniProt: P00797, renin
#2: Chemical ChemComp-C40 / N-[(2R,4S,5S,7R)-4-AMINO-8-(BUTYLAMINO)-5-HYDROXY-2,7-DIMETHYL-8-OXOOCTYL]-2-(3-METHOXYPROPOXY)BENZAMIDE


Mass: 465.626 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C25H43N3O5
Has protein modificationY

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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: 3.1 Å3/Da / Density % sol: 60.38 % / Description: NONE
Crystal growpH: 3 / Details: pH 3

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: ENRAF-NONIUS FR571 / Wavelength: 1.5418
DetectorType: DELFT / Detector: AREA DETECTOR / Date: Jan 1, 1993
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.9→10 Å / Num. obs: 10676 / % possible obs: 98 % / Observed criterion σ(I): 3 / Redundancy: 3.58 % / Rmerge(I) obs: 0.06

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Processing

Software
NameClassification
X-PLORrefinement
MADNESSdata reduction
RefinementMethod to determine structure: OTHER
Starting model: NONE

Resolution: 2.8→10 Å / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflection
Rwork0.228 --
obs0.228 10398 98 %
Refinement stepCycle: LAST / Resolution: 2.8→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2500 0 33 0 2533
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.022
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_deg3.73
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d26.6
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

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