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- PDB-3vyf: Human renin in complex with inhibitor 9 -

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Basic information

Entry
Database: PDB / ID: 3vyf
TitleHuman renin in complex with inhibitor 9
ComponentsRenin
KeywordsHYDROLASE/HYDROLASE INHIBITOR / Aspartyl protease / RAS / hypertension / inhibitor / 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 / amyloid-beta metabolic process ...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 / amyloid-beta metabolic process / Metabolism of Angiotensinogen to Angiotensins / cell maturation / response to cAMP / hormone-mediated signaling pathway / kidney development / insulin-like growth factor receptor binding / 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 discovery of new (3S,5R)-5-[4-(2-chlorophenyl)-2,2-dimethyl-5-oxopiperazin-1-yl]piperidine-3-carboxamides as potent renin inhibitors
Authors: Mori, Y. / Ogawa, Y. / Mochizuki, A. / Nakamura, Y. / Sugita, C. / Miyazaki, S. / Tamaki, K. / Matsui, Y. / Takahashi, M. / Nagayama, T. / Nagai, Y. / Inoue, S. / Nishi, T.
History
DepositionSep 24, 2012Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 19, 2012Provider: repository / Type: Initial release
Revision 1.1Jul 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 1.2Nov 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)75,9596
Polymers74,5342
Non-polymers1,4254
Water1,74797
1
A: Renin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,9793
Polymers37,2671
Non-polymers7122
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Renin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,9793
Polymers37,2671
Non-polymers7122
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)227,87618
Polymers223,6026
Non-polymers4,27412
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_577z+1/2,-x+5/2,-y+21
crystal symmetry operation12_774-y+5/2,-z+2,x-1/21
Buried area13570 Å2
ΔGint-52 kcal/mol
Surface area73410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)141.427, 141.427, 141.427
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


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-VYF / (3S,5R)-5-[4-(2-chlorophenyl)-2,2-dimethyl-5-oxopiperazin-1-yl]-N-(2,6-dimethylheptan-4-yl)piperidine-3-carboxamide


Mass: 491.109 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H43ClN4O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 97 / 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: 3.16 Å3/Da / Density % sol: 61.11 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop
Details: 5-12% PEG 3350, 0.6M NaCl, 0.1M citrate pH3.0-4.5, vapor diffusion, hanging drop, temperature 295K, VAPOR DIFFUSION, HANGING DROP
PH range: 3.0-4.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.502 Å
DetectorType: RIGAKU RAXIS VII / Detector: IMAGE PLATE / Date: Aug 13, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.502 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. obs: 23593 / % possible obs: 99.9 % / Redundancy: 5.2 % / Biso Wilson estimate: 83.1 Å2

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Processing

Software
NameVersionClassificationNB
CNS1.2refinement
PDB_EXTRACT3.11data extraction
CrystalCleardata collection
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3VSW

3vsw


Resolution: 2.8→19.8 Å / Rfactor Rfree error: 0.006 / Occupancy max: 1 / Occupancy min: 0.25 / Data cutoff high absF: 1684691 / 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
Rfree0.266 2328 10 %RANDOM
Rwork0.218 ---
obs-23333 99.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 33.6743 Å2 / ksol: 0.35 e/Å3
Displacement parametersBiso max: 90.62 Å2 / Biso mean: 42.5212 Å2 / Biso min: 10.08 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.45 Å0.35 Å
Luzzati d res low-5 Å
Luzzati sigma a0.52 Å0.41 Å
Refinement stepCycle: LAST / Resolution: 2.8→19.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5170 0 96 97 5363
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d31.5
X-RAY DIFFRACTIONc_improper_angle_d0.71
X-RAY DIFFRACTIONc_mcbond_it1.211.5
X-RAY DIFFRACTIONc_mcangle_it2.042
X-RAY DIFFRACTIONc_scbond_it1.812
X-RAY DIFFRACTIONc_scangle_it2.792.5
LS refinement shellResolution: 2.8→2.97 Å / Rfactor Rfree error: 0.021 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.407 381 9.9 %
Rwork0.316 3469 -
all-3850 -
obs--99.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water.paramwater.top
X-RAY DIFFRACTION3UNL.paramUNL.top
X-RAY DIFFRACTION4carbohydrate.paramcarbohydrate.top

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