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- PDB-3vsw: Human renin in complex with compound 8 -

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Basic information

Entry
Database: PDB / ID: 3vsw
TitleHuman renin in complex with compound 8
ComponentsRenin
KeywordsHYDROLASE/HYDROLASE INHIBITOR / RAS / hypertension / inhibitor / Aspartyl protease / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


renin / mesonephros development / juxtaglomerular apparatus development / response to cGMP / renin-angiotensin regulation of aldosterone production / drinking behavior / response to immobilization stress / regulation of MAPK cascade / response to cAMP / amyloid-beta metabolic process ...renin / mesonephros development / juxtaglomerular apparatus development / response to cGMP / renin-angiotensin regulation of aldosterone production / drinking behavior / response to immobilization stress / regulation of MAPK cascade / response to cAMP / amyloid-beta metabolic process / Metabolism of Angiotensinogen to Angiotensins / cell maturation / angiotensin maturation / hormone-mediated signaling pathway / insulin-like growth factor receptor binding / 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: 3 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
Revision 1.4Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)76,0766
Polymers74,5342
Non-polymers1,5424
Water00
1
A: Renin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,0383
Polymers37,2671
Non-polymers7712
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Renin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,0383
Polymers37,2671
Non-polymers7712
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)228,22818
Polymers223,6026
Non-polymers4,62512
Water0
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 area15370 Å2
ΔGint-51 kcal/mol
Surface area72300 Å2
MethodPISA
4
A: Renin
hetero molecules

A: Renin
hetero molecules

A: Renin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,1149
Polymers111,8013
Non-polymers2,3136
Water0
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 area4170 Å2
ΔGint-21 kcal/mol
Surface area39060 Å2
MethodPISA
5
B: Renin
hetero molecules

B: Renin
hetero molecules

B: Renin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,1149
Polymers111,8013
Non-polymers2,3136
Water0
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 area4640 Å2
ΔGint-20 kcal/mol
Surface area39810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)140.762, 140.762, 140.762
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-R31 / (2S,4S,5S)-5-amino-N-(3-amino-2,2-dimethyl-3-oxopropyl)-4-hydroxy-6-{4-[2-(3-methoxypropoxy)phenyl]-3-oxopiperazin-1-yl}-2-(propan-2-yl)hexanamide


Mass: 549.703 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C28H47N5O6
Has protein modificationY

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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: 3.12 Å3/Da / Density % sol: 60.56 % / Mosaicity: 0.827 °
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 3
Details: 5-12% PEG 3350, 0.6M NaCl, 0.1M citrate (pH3.0-4.5), 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: Feb 14, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 3→50 Å / Num. obs: 18881 / % possible obs: 99.6 % / Redundancy: 5.6 % / Rmerge(I) obs: 0.053 / Χ2: 1.677 / Net I/σ(I): 28.2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
3-3.115.60.17418591.479199.8
3.11-3.235.60.14118681.542199.9
3.23-3.385.60.10318851.592199.9
3.38-3.565.70.07718741.593199.9
3.56-3.785.60.06218521.726199.9
3.78-4.075.60.0518811.703199.6
4.07-4.485.60.03818941.667199.8
4.48-5.135.60.03218971.907199.6
5.13-6.465.60.03619141.605199.7
6.46-505.40.02919571.958197.7

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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: 3→19.91 Å / Rfactor Rfree error: 0.007 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.7332 / Data cutoff high absF: 1661881 / 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
Rfree0.309 1870 10 %OTHER
Rwork0.235 ---
obs-18741 99.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 15.618 Å2 / ksol: 0.3285 e/Å3
Displacement parametersBiso max: 74.75 Å2 / Biso mean: 29.8287 Å2 / Biso min: 8.18 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.57 Å0.39 Å
Luzzati d res low-5 Å
Luzzati sigma a0.63 Å0.48 Å
Refinement stepCycle: LAST / Resolution: 3→19.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5242 0 106 0 5348
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d26.3
X-RAY DIFFRACTIONc_improper_angle_d0.8
X-RAY DIFFRACTIONc_mcbond_it1.071.5
X-RAY DIFFRACTIONc_mcangle_it1.882
X-RAY DIFFRACTIONc_scbond_it1.492
X-RAY DIFFRACTIONc_scangle_it2.372.5
LS refinement shellResolution: 3→3.19 Å / Rfactor Rfree error: 0.023 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.416 322 10.5 %
Rwork0.343 2748 -
all-3070 -
obs--99.6 %
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 DIFFRACTION4UNL.paramUNL.top

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