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- PDB-5v8v: Crystal Structure of Human Renin in Complex with a biphenylpipder... -

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Basic information

Entry
Database: PDB / ID: 5v8v
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 / 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
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
DepositionMar 22, 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
Revision 1.3Oct 4, 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

Downloads & links

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Assembly

Deposited unit
A: Renin
B: Renin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,4328
Polymers73,8792
Non-polymers2,5536
Water1,24369
1
A: Renin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,2164
Polymers36,9401
Non-polymers1,2773
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Renin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,2164
Polymers36,9401
Non-polymers1,2773
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)54.367, 99.014, 147.031
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(0.50041, -0.861258, -0.088455), (-0.864659, -0.491923, -0.10187), (0.044224, 0.12746, -0.990857)41.63481, 71.12656, 34.11816

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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 (production host): HEK-F / Production host: Baculoviridae (virus) / 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: obtained synthetically / 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-90D / methyl [(4S)-4-(3'-ethyl-6-fluoro[1,1'-biphenyl]-2-yl)-4-hydroxy-4-{(3R)-1-[4-(methylamino)butanoyl]piperidin-3-yl}butyl]carbamate


Mass: 527.671 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C30H42FN3O4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 69 / 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: 2.7 Å3/Da / Density % sol: 54.51 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 19-22% PEG3350, 200mM ammonium sulfate, 100mM TRIS-HCl, pH 7.5, 2mM inhibitor, 1% DMSO
PH range: 7.0 - 8.5

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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: Jun 20, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 25373 / % possible obs: 99.6 % / Observed criterion σ(I): 2 / Redundancy: 4.6 % / Rmerge(I) obs: 0.0118 / Net I/σ(I): 6.7

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4ryc

4ryc


Resolution: 2.6→45.334 Å / SU ML: 0.39 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 25.74 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2533 1406 5.91 %RANDOM
Rwork0.1858 ---
obs0.1897 23801 94.6 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.6→45.334 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5106 0 180 69 5355
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0055421
X-RAY DIFFRACTIONf_angle_d0.7647371
X-RAY DIFFRACTIONf_dihedral_angle_d14.7943104
X-RAY DIFFRACTIONf_chiral_restr0.052820
X-RAY DIFFRACTIONf_plane_restr0.004928
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.69290.39761150.33031868X-RAY DIFFRACTION80
2.6929-2.80070.39621440.27082067X-RAY DIFFRACTION90
2.8007-2.92820.29881470.23552118X-RAY DIFFRACTION92
2.9282-3.08250.29041250.22142245X-RAY DIFFRACTION95
3.0825-3.27560.3241330.2172284X-RAY DIFFRACTION97
3.2756-3.52840.25431400.20232283X-RAY DIFFRACTION97
3.5284-3.88330.25121520.17282313X-RAY DIFFRACTION98
3.8833-4.44480.21081430.13992332X-RAY DIFFRACTION98
4.4448-5.59840.17581530.13522401X-RAY DIFFRACTION99
5.5984-45.34070.22881540.17712484X-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)
10.86480.05610.03540.3377-0.12731.10060.01050.00290.094-0.01470.0782-0.0088-0.04860.04450.00080.1299-0.014-0.00360.0883-0.04190.164529.697246.13749.2184
20.53230.3738-0.03130.7507-0.36370.9045-0.0607-0.1584-0.02540.04880.13510.0964-0.074-0.14660.00550.15350.05210.00270.18960.05130.135714.520519.402328.2006
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A
2X-RAY DIFFRACTION2chain B

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