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- PDB-5vrp: Crystal Structure of Human Renin in Complex with a biphenylpipder... -

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Basic information

Entry
Database: PDB / ID: 5vrp
TitleCrystal Structure of Human Renin in Complex with a biphenylpipderidinylcarbinol
ComponentsRenin
KeywordsHYDROLASE/HYDROLASE inhibitor / renin inhibitor / biphenyl / hypertension / Cyp 3A4 / 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 / SYNCHROTRON / Resolution: 3.22 Å
AuthorsConcha, N. / Zhao, B.
CitationJournal: Bioorg. Med. Chem. Lett. / Year: 2017
Title: Discovery of renin inhibitors containing a simple aspartate binding moiety that imparts reduced P450 inhibition.
Authors: Lawhorn, B.G. / Tran, T. / Hong, V.S. / Morgan, L.A. / Le, B.T. / Harpel, M.R. / Jolivette, L. / Diaz, E. / Schwartz, B. / Gross, J.W. / Tomaszek, T. / Semus, S. / Concha, N. / Smallwood, A. ...Authors: Lawhorn, B.G. / Tran, T. / Hong, V.S. / Morgan, L.A. / Le, B.T. / Harpel, M.R. / Jolivette, L. / Diaz, E. / Schwartz, B. / Gross, J.W. / Tomaszek, T. / Semus, S. / Concha, N. / Smallwood, A. / Holt, D.A. / Kallander, L.S.
History
DepositionMay 11, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 18, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 25, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
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_role
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)76,5369
Polymers73,8792
Non-polymers2,6577
Water181
1
A: Renin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,3165
Polymers36,9401
Non-polymers1,3774
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Renin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,2204
Polymers36,9401
Non-polymers1,2803
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2430 Å2
ΔGint-15 kcal/mol
Surface area26470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.334, 99.933, 146.529
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Renin / Angiotensinogenase


Mass: 36939.594 Da / Num. of mol.: 2 / Fragment: UNP residues 70-406
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: REN / Cell line (production host): HEK-F / Production host: Homo sapiens (human) / References: UniProt: P00797, renin
#2: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose


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-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-9JD / methyl [(4S)-4-{(3R)-1-[(3S)-4-amino-3-hydroxybutanoyl]piperidin-3-yl}-4-(3'-ethyl-6-fluoro[1,1'-biphenyl]-2-yl)-4-hydroxybutyl]carbamate


Mass: 529.643 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C29H40FN3O5
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1 / 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: 2.69 Å3/Da / Density % sol: 54.31 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 1 ul of 200 mM inhibitor solution in DMSO was added to 100 ul of protein.. The inhibitor was soluble in the protein solution. The inhibitor stock was freshly made. The sample was incubated ...Details: 1 ul of 200 mM inhibitor solution in DMSO was added to 100 ul of protein.. The inhibitor was soluble in the protein solution. The inhibitor stock was freshly made. The sample was incubated for 3 hr on ice prior to setting up the plates. 2 ml protein, 2 ml well hanging drops were set up in the cold. Streak seeded the next day with crushed crystals from the last time.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Aug 1, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.22→50 Å / Num. obs: 13533 / % possible obs: 99.9 % / Redundancy: 6.7 % / Net I/σ(I): 6

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Processing

Software
NameVersionClassification
PHENIX(1.10_2155: ???)refinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementResolution: 3.22→24.983 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 0.08 / Phase error: 23.9 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2624 704 5.9 %
Rwork0.2455 --
obs0.2464 11935 88.63 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.22→24.983 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5021 0 185 1 5207
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0045348
X-RAY DIFFRACTIONf_angle_d0.6647279
X-RAY DIFFRACTIONf_dihedral_angle_d17.1233052
X-RAY DIFFRACTIONf_chiral_restr0.048813
X-RAY DIFFRACTIONf_plane_restr0.003915
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2203-3.46830.33321260.33291999X-RAY DIFFRACTION81
3.4683-3.81630.29011120.30952013X-RAY DIFFRACTION81
3.8163-4.36590.23671410.25172177X-RAY DIFFRACTION87
4.3659-5.4910.2211600.2032441X-RAY DIFFRACTION96
5.491-24.9840.28031650.21952601X-RAY DIFFRACTION98
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.2322-0.60841.91990.7767-1.01423.1533-0.0052-0.07390.11430.08580.0752-0.0443-0.2297-0.0073-0.06940.322-0.00960.01950.2721-0.11190.380829.64246.48238.9386
23.06070.6589-0.57292.4762-0.13062.6084-0.0752-0.30780.18420.21290.24530.2354-0.2996-0.5061-0.09540.39070.1075-0.00570.48750.07410.272114.623419.313828.207
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 70:326 )A70 - 326
2X-RAY DIFFRACTION2( CHAIN B AND RESID 70:326 )B70 - 326

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