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

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Basic information

Entry
Database: PDB / ID: 5vpm
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 / amyloid-beta metabolic process / angiotensin maturation ...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 / amyloid-beta metabolic process / angiotensin maturation / 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: 2.9 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 5, 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 23, 2024Group: 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_entry_details / pdbx_modification_feature / struct_ncs_dom_lim
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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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)75,6218
Polymers73,8792
Non-polymers1,7426
Water18010
1
A: Renin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,8114
Polymers36,9401
Non-polymers8713
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Renin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,8114
Polymers36,9401
Non-polymers8713
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)55.378, 103.847, 145.520
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: GLY / Beg label comp-ID: GLY / End auth comp-ID: ARG / End label comp-ID: ARG / Refine code: 5 / Auth seq-ID: 1 - 337 / Label seq-ID: 1 - 337

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(0.532947, 0.83735, -0.121702), (0.845432, -0.52104, 0.117316), (0.034823, -0.165414, -0.985609)27.87502, -52.87689, -43.77201

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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 / 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-9G7 / methyl [(4S)-4-(3'-ethyl-6-fluoro[1,1'-biphenyl]-2-yl)-4-hydroxy-4-{(3R)-1-[(piperidin-4-yl)acetyl]piperidin-3-yl}butyl]carbamate


Mass: 553.708 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C32H44FN3O4
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 10 / Source method: isolated from a natural source / Formula: H2O
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: 2.83 Å3/Da / Density % sol: 56.57 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 19-22% PEG3350, 0.2M ammonium sulfate, 0.1M TRIS-HCl, pH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: RAYONIX MX-225 / 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: 2.9→50 Å / Num. obs: 15929 / % possible obs: 82.5 % / Redundancy: 5.2 % / Net I/σ(I): 10.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.9→50 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.884 / SU B: 44.237 / SU ML: 0.376 / Cross valid method: THROUGHOUT / ESU R Free: 0.482 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26045 831 5.2 %RANDOM
Rwork0.20158 ---
obs0.20473 15066 82.4 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 58.345 Å2
Baniso -1Baniso -2Baniso -3
1--0.96 Å20 Å20 Å2
2--2.94 Å2-0 Å2
3----1.98 Å2
Refinement stepCycle: 1 / Resolution: 2.9→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5081 0 118 10 5209
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.025327
X-RAY DIFFRACTIONr_bond_other_d0.0030.024731
X-RAY DIFFRACTIONr_angle_refined_deg1.3351.9527242
X-RAY DIFFRACTIONr_angle_other_deg0.9042.99310987
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2235665
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.69524.366213
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.87515806
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.1041516
X-RAY DIFFRACTIONr_chiral_restr0.0750.2815
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.025903
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021095
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.2154.7472672
X-RAY DIFFRACTIONr_mcbond_other1.2154.7462671
X-RAY DIFFRACTIONr_mcangle_it2.1287.1153333
X-RAY DIFFRACTIONr_mcangle_other2.1277.1153334
X-RAY DIFFRACTIONr_scbond_it1.0844.8212655
X-RAY DIFFRACTIONr_scbond_other1.0764.8082648
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.9027.1833898
X-RAY DIFFRACTIONr_long_range_B_refined3.50854.3645611
X-RAY DIFFRACTIONr_long_range_B_other3.41854.3665611
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

NumberTypeRms dev position (Å)Weight position
1957medium positional0.210.5
2822loose positional0.685
1957medium thermal4.342
2822loose thermal4.5410
LS refinement shellResolution: 2.9→2.975 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.389 32 -
Rwork0.364 601 -
obs--45.44 %
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)
10.7734-0.12780.62030.37620.07891.686-0.0115-0.09530.1163-0.06280.08280.04710.00660.0893-0.07130.0143-0.0059-0.02080.0538-0.05190.116325.4791-3.9373-9.4436
20.9469-0.324-0.41050.7213-0.10710.6272-0.0802-0.2111-0.0004-0.10880.1579-0.0106-0.00810.0759-0.07770.064-0.01190.02940.1133-0.06030.074741.2617-33.3716-27.9753
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 337
2X-RAY DIFFRACTION2B1 - 337

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