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- PDB-2v11: Crystal Structure of Renin with Inhibitor 6 -

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Entry
Database: PDB / ID: 2v11
TitleCrystal Structure of Renin with Inhibitor 6
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


Metabolism of Angiotensinogen to Angiotensins / response to cGMP / renin / renin-angiotensin regulation of aldosterone production / mesonephros development / drinking behavior / angiotensin maturation / regulation of MAPK cascade / response to cAMP / hormone-mediated signaling pathway ...Metabolism of Angiotensinogen to Angiotensins / response to cGMP / renin / renin-angiotensin regulation of aldosterone production / mesonephros development / drinking behavior / angiotensin maturation / regulation of MAPK cascade / response to cAMP / hormone-mediated signaling pathway / cell maturation / amyloid-beta metabolic process / insulin-like growth factor receptor binding / response to immobilization stress / cellular response to drug / regulation of blood pressure / male gonad development / kidney development / apical part of cell / peptidase activity / response to lipopolysaccharide / aspartic-type endopeptidase activity / proteolysis / signaling receptor binding / extracellular space / extracellular region / plasma membrane / cytoplasm
Renin-like domain / Peptidase family A1 domain / Aspartic peptidase A1 family / Aspartic peptidase, active site / Peptidase family A1 domain profile. / Aspartic peptidase, N-terminal / Eukaryotic and viral aspartyl proteases active site. / A1 Propeptide / Eukaryotic aspartyl protease / Aspartic peptidase domain superfamily
Renin
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / OTHER / Resolution: 3.1 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.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: May 21, 2007 / Release: Jul 3, 2007
RevisionDateData content typeGroupCategoryItemProviderType
1.0Jul 3, 2007Structure modelrepositoryInitial release
1.1May 8, 2011Structure modelVersion format compliance
1.2Jul 13, 2011Structure modelVersion format compliance
1.3Jun 28, 2017Structure modelData collectiondiffrn_source_diffrn_source.type
1.4Jul 12, 2017Structure modelRefinement descriptionsoftware_software.name
1.5Apr 3, 2019Structure modelData collection / Source and taxonomyentity_src_gen_entity_src_gen.pdbx_host_org_cell_line
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
C: RENIN
O: RENIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,5494
Polymers74,5342
Non-polymers1,0152
Water0
1
C: RENIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,7752
Polymers37,2671
Non-polymers5081
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
O: RENIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,7752
Polymers37,2671
Non-polymers5081
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
γ
α
β
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

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Components

#1: Protein/peptide RENIN / / ANGIOTENSINOGENASE


Mass: 37267.008 Da / Num. of mol.: 2
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-C80 / (2S,4S,5R,7R)-4-AMINO-8-(BUTYLAMINO)-5-HYDROXY-2,7-DIMETHYL-8-OXOOCTYL 1-BENZYL-1H-INDOLE-3-CARBOXYLATE


Mass: 507.664 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C30H41N3O4

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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: 3.26 Å3/Da / Density % sol: 62.3 %
Crystal growpH: 3 / Details: pH 3.00

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: ENRAF-NONIUS FR571 / Wavelength: 1.5418
DetectorType: DELFT INSTRUMENTS / 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: 3.1→10 Å / Num. obs: 17263 / % possible obs: 96 % / Observed criterion σ(I): 3 / Redundancy: 3.3 % / Rmerge(I) obs: 0.22

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Processing

Software
NameClassification
X-PLORrefinement
MADNESSdata reduction
RefinementMethod to determine structure: OTHER / Resolution: 3.1→10 Å / Cross valid method: THROUGHOUT / σ(F): 2
Details: B-FACTORS WERE NOT REFINED AND A CONSTANT VALUE IS ASSIGNED IN THE COORDINATE-FILE
RfactorNum. reflection% reflection
Rwork0.217 --
Obs0.217 17263 96 %
Refinement stepCycle: LAST / Resolution: 3.1→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5124 0 74 0 5198
Refine LS restraints
Refinement-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.019
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_deg3.673
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d27.33
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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