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- PDB-4rz1: RENIN IN COMPLEXED WITH (3S,4S)-4-({[4-methoxy-3-(3-methoxypropox... -

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Basic information

Entry
Database: PDB / ID: 4rz1
TitleRENIN IN COMPLEXED WITH (3S,4S)-4-({[4-methoxy-3-(3-methoxypropoxy)benzoyl](propan-2-yl)amino}methyl)pyrrolidin-3-yl benzylcarbamate INHIBITOR
ComponentsRenin
KeywordsHYDROLASE/HYDROLASE INHIBITOR / HYDROLASE / HYDROLASE-HYDROLASE INHIBITOR complex
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsOstermann, N.
CitationJournal: Bioorg.Med.Chem.Lett. / Year: 2015
Title: trans-3,4-Disubstituted pyrrolidines as inhibitors of the human aspartyl protease renin. Part II: Prime site exploration using an oxygen linker.
Authors: Sellner, H. / Cottens, S. / Cumin, F. / Ehrhardt, C. / Kosaka, T. / Lorthiois, E. / Ostermann, N. / Webb, R.L. / Rigel, D.F. / Wagner, T. / Maibaum, J.
History
DepositionDec 18, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 25, 2015Provider: repository / Type: Initial release
Revision 1.1Apr 22, 2015Group: Database references
Revision 1.2Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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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)76,2569
Polymers74,5342
Non-polymers1,7227
Water3,207178
1
A: Renin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,0984
Polymers37,2671
Non-polymers8313
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Renin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,1585
Polymers37,2671
Non-polymers8914
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: Renin
B: Renin
hetero molecules

A: Renin
B: Renin
hetero molecules

A: Renin
B: Renin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)228,76827
Polymers223,6026
Non-polymers5,16621
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_564-z+1/2,-x+1,y-1/21
crystal symmetry operation10_655-y+1,z+1/2,-x+1/21
Buried area16920 Å2
ΔGint-90 kcal/mol
Surface area73420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)141.294, 141.294, 141.294
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number198
Space group name H-MP213

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Components

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Protein / Sugars , 2 types, 4 molecules AB

#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) / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: P00797, renin
#2: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 4 types, 183 molecules

#3: Chemical ChemComp-3ZN / (3S,4S)-4-({[4-methoxy-3-(3-methoxypropoxy)benzoyl](propan-2-yl)amino}methyl)pyrrolidin-3-yl benzylcarbamate


Mass: 513.626 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C28H39N3O6
#4: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE / Dimethyl sulfoxide


Mass: 78.133 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 178 / Source method: isolated from a natural source / Formula: H2O

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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: 3.15 Å3/Da / Density % sol: 61 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4
Details: REMARK: HANGING DROP, VAPOR DIFFUSION, 1 UL PROTEIN + 1 UL RESERVOIR; PROTEIN SOLUTION: 9.4 MG/ML RENIN, 12.5 MM TRIS PH 8, 25 MM NACL; RESERVOIR SOLUTION: 21% PEG4000, 50 MM NACITRATE PH 4. ...Details: REMARK: HANGING DROP, VAPOR DIFFUSION, 1 UL PROTEIN + 1 UL RESERVOIR; PROTEIN SOLUTION: 9.4 MG/ML RENIN, 12.5 MM TRIS PH 8, 25 MM NACL; RESERVOIR SOLUTION: 21% PEG4000, 50 MM NACITRATE PH 4.0, 400 MM NACL; SOAKING: DROP PLUS 2.5 UL RESERVOIR SOLUTION PLUS 10 MM compound AND 10% DMSO FOR 20 MIN; CRYO: SOAKING SOLUTION PLUS 15% GLYCEROL, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.97865 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 18, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97865 Å / Relative weight: 1
ReflectionResolution: 2.6→33 Å / Num. all: 29045 / Num. obs: 29045 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Biso Wilson estimate: 71.93 Å2
Reflection shellResolution: 2.6→2.69 Å / % possible all: 100

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Processing

Software
NameVersionClassification
BUSTER2.11.4refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→32.41 Å / Cor.coef. Fo:Fc: 0.9418 / Cor.coef. Fo:Fc free: 0.9283 / SU R Cruickshank DPI: 0.453 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.2271 2929 10.11 %RANDOM
Rwork0.199 ---
obs0.2019 28975 99.44 %-
all-28975 --
Displacement parametersBiso mean: 56.94 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyzeLuzzati coordinate error obs: 0.341 Å
Refinement stepCycle: LAST / Resolution: 2.6→32.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5170 0 115 178 5463
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.015412HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.27344HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1810SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes110HARMONIC2
X-RAY DIFFRACTIONt_gen_planes792HARMONIC5
X-RAY DIFFRACTIONt_it5412HARMONIC20
X-RAY DIFFRACTIONt_omega_torsion3.61
X-RAY DIFFRACTIONt_other_torsion18.99
X-RAY DIFFRACTIONt_chiral_improper_torsion722SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact6051SEMIHARMONIC4
LS refinement shellResolution: 2.6→2.69 Å / Total num. of bins used: 15
RfactorNum. reflection% reflection
Rfree0.3079 298 10.94 %
Rwork0.2521 2425 -
all0.2583 2723 -
obs--99.44 %

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