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- PDB-3vsx: Human renin in complex with compound 18 -

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Basic information

Entry
Database: PDB / ID: 3vsx
TitleHuman renin in complex with compound 18
ComponentsRenin
KeywordsHYDROLASE/HYDROLASE INHIBITOR / RAS / hypertension / inhibitor / Aspartyl protease / 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 / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsTakahashi, M. / Hanzawa, H.
CitationJournal: Bioorg.Med.Chem.Lett. / Year: 2012
Title: Design and optimization of novel (2S,4S,5S)-5-amino-6-(2,2-dimethyl-5-oxo-4-phenylpiperazin-1-yl)-4-hydroxy-2-isopropylhexanamides as renin inhibitors
Authors: Nakamura, Y. / Sugita, C. / Meguro, M. / Miyazaki, S. / Tamaki, K. / Takahashi, M. / Nagai, Y. / Nagayama, T. / Kato, M. / Suemune, H. / Nishi, T.
History
DepositionMay 11, 2012Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 25, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Refinement description / Category: software
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
Revision 1.3Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Renin
B: Renin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,0256
Polymers74,5342
Non-polymers1,4914
Water0
1
A: Renin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,0123
Polymers37,2671
Non-polymers7452
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Renin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,0123
Polymers37,2671
Non-polymers7452
Water0
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)228,07418
Polymers223,6026
Non-polymers4,47212
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_533z+1/2,-x-3/2,-y-21
crystal symmetry operation12_334-y-3/2,-z-2,x-1/21
Buried area16180 Å2
ΔGint-51 kcal/mol
Surface area71630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)138.188, 138.188, 138.188
Angle α, β, γ (deg.)90.000, 90.000, 90.000
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) / Gene: REN / Plasmid: pcDNA3.1 / Cell line (production host): 293F / Production host: Homo sapiens (human) / References: UniProt: P00797, renin
#2: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE / 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
#3: Chemical ChemComp-R32 / (2S,4S,5S)-5-amino-N-(3-amino-2,2-dimethyl-3-oxopropyl)-6-[4-(2-chlorophenyl)-2,2-dimethyl-5-oxopiperazin-1-yl]-4-hydroxy-2-(propan-2-yl)hexanamide


Mass: 524.096 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C26H42ClN5O4

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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: 2.95 Å3/Da / Density % sol: 58.31 % / Mosaicity: 0.618 °
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 3
Details: 5-12% PEG3 350, 0.6M NaCl, 0.1M citrate (pH 3.0-4.5), VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E DW
DetectorType: RIGAKU RAXIS VII / Detector: IMAGE PLATE / Date: Apr 12, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.8→50 Å / Num. obs: 21771 / % possible obs: 98.9 % / Redundancy: 6.2 % / Rmerge(I) obs: 0.125 / Χ2: 2.198 / Net I/σ(I): 25.1
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.8-2.96.50.24121451.7261100
2.9-3.026.50.2121881.8351100
3.02-3.156.50.19221892.0141100
3.15-3.326.50.16621612.2231100
3.32-3.536.50.14921912.238199.9
3.53-3.86.30.13421792.212199.7
3.8-4.185.90.12721612.44198.4
4.18-4.795.30.11421102.476195.7
4.79-6.035.80.10721662.431197.7
6.03-506.10.07822812.522198.1

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
PDB_EXTRACT3.11data extraction
CrystalCleardata collection
HKL-2000data scaling
CNX2000.1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1RNE

1rne


Resolution: 2.8→19.74 Å / Rfactor Rfree error: 0.006 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.7621 / Data cutoff high absF: 1545152 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.301 2165 10 %OTHER
Rwork0.237 ---
obs-21665 99 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 10 Å2 / ksol: 0.2759 e/Å3
Displacement parametersBiso max: 70.77 Å2 / Biso mean: 32.5614 Å2 / Biso min: 9.92 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.49 Å0.37 Å
Luzzati d res low-5 Å
Luzzati sigma a0.59 Å0.4 Å
Refinement stepCycle: LAST / Resolution: 2.8→19.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5240 0 100 0 5340
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d26.6
X-RAY DIFFRACTIONc_improper_angle_d0.87
X-RAY DIFFRACTIONc_mcbond_it1.091.5
X-RAY DIFFRACTIONc_mcangle_it1.892
X-RAY DIFFRACTIONc_scbond_it1.52
X-RAY DIFFRACTIONc_scangle_it2.342.5
LS refinement shellResolution: 2.8→2.97 Å / Rfactor Rfree error: 0.023 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.438 354 9.8 %
Rwork0.336 3243 -
all-3597 -
obs--100 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water.paramwater.top
X-RAY DIFFRACTION3carbohydrate.paramcarbohydrate.top
X-RAY DIFFRACTION4R32.paramR32.top

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