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- PDB-2v10: Crystal Structure of Renin with Inhibitor 9 -

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Basic information

Entry
Database: PDB / ID: 2v10
TitleCrystal Structure of Renin with Inhibitor 9
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 / renin-angiotensin regulation of aldosterone production / drinking behavior / regulation of MAPK cascade / response to immobilization stress / angiotensin maturation / Metabolism of Angiotensinogen to Angiotensins ...renin / juxtaglomerular apparatus development / mesonephros development / response to cGMP / renin-angiotensin regulation of aldosterone production / drinking behavior / regulation of MAPK cascade / response to immobilization stress / angiotensin maturation / Metabolism of Angiotensinogen to Angiotensins / amyloid-beta metabolic process / cell maturation / response to cAMP / insulin-like growth factor receptor binding / hormone-mediated signaling pathway / 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 / 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.
History
DepositionMay 21, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 3, 2007Provider: 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
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)75,4954
Polymers74,5342
Non-polymers9612
Water0
1
C: RENIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,7482
Polymers37,2671
Non-polymers4811
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
O: RENIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,7482
Polymers37,2671
Non-polymers4811
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)143.000, 143.000, 143.000
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 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-C61 / (2R,4S,5S,7S)-5-AMINO-N-BUTYL-4-HYDROXY-7-[4-METHOXY-3-(3-METHOXYPROPOXY)BENZYL]-2,8-DIMETHYLNONANAMIDE


Mass: 480.680 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H48N2O5

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.27 Å3/Da / Density % sol: 62.38 %
Crystal growpH: 4.5 / Details: pH 4.50

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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, 1991
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: 17734 / % possible obs: 99 % / Observed criterion σ(I): 0 / Redundancy: 3.35 % / Rmerge(I) obs: 0.12

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Processing

Software
NameClassification
TNTrefinement
MADNESSdata reduction
RefinementMethod to determine structure: OTHER / Resolution: 3.1→10 Å / Cross valid method: THROUGHOUT / σ(F): 0
Details: B-FACTORS WERE NOT REFINED AND A CONSTANT VALUE IS ASSIGNED IN THE COORDINATE-FILE
RfactorNum. reflection
Rwork0.21 -
obs0.21 17183
Refinement stepCycle: LAST / Resolution: 3.1→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5124 0 68 0 5192

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