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- PDB-9gbl: Human Angiotensin-1 converting enzyme C-domain in complex with a ... -

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Basic information

Entry
Database: PDB / ID: 9gbl
TitleHuman Angiotensin-1 converting enzyme C-domain in complex with a diprolyl inhibitor- SG18
ComponentsAngiotensin-converting enzyme
KeywordsHYDROLASE / Inhibitor / complex / protease
Function / homology
Function and homology information


mononuclear cell proliferation / cell proliferation in bone marrow / bradykinin receptor binding / exopeptidase activity / regulation of angiotensin metabolic process / substance P catabolic process / tripeptidyl-peptidase activity / peptidyl-dipeptidase A / regulation of renal output by angiotensin / negative regulation of gap junction assembly ...mononuclear cell proliferation / cell proliferation in bone marrow / bradykinin receptor binding / exopeptidase activity / regulation of angiotensin metabolic process / substance P catabolic process / tripeptidyl-peptidase activity / peptidyl-dipeptidase A / regulation of renal output by angiotensin / negative regulation of gap junction assembly / hormone catabolic process / bradykinin catabolic process / metallodipeptidase activity / regulation of smooth muscle cell migration / regulation of hematopoietic stem cell proliferation / neutrophil mediated immunity / hormone metabolic process / mitogen-activated protein kinase binding / mitogen-activated protein kinase kinase binding / chloride ion binding / arachidonate secretion / post-transcriptional regulation of gene expression / peptide catabolic process / heart contraction / positive regulation of systemic arterial blood pressure / antigen processing and presentation of peptide antigen via MHC class I / regulation of heart rate by cardiac conduction / regulation of systemic arterial blood pressure by renin-angiotensin / blood vessel remodeling / amyloid-beta metabolic process / hematopoietic stem cell differentiation / peptidyl-dipeptidase activity / regulation of vasoconstriction / Metabolism of Angiotensinogen to Angiotensins / angiotensin maturation / metallocarboxypeptidase activity / blood vessel diameter maintenance / angiotensin-activated signaling pathway / kidney development / regulation of synaptic plasticity / metalloendopeptidase activity / regulation of blood pressure / male gonad development / metallopeptidase activity / peptidase activity / actin binding / spermatogenesis / endopeptidase activity / calmodulin binding / lysosome / endosome / negative regulation of gene expression / external side of plasma membrane / proteolysis / extracellular space / extracellular exosome / extracellular region / zinc ion binding / plasma membrane
Similarity search - Function
Peptidase M2, peptidyl-dipeptidase A / Angiotensin-converting enzyme / Peptidase family M2 domain profile. / Neutral zinc metallopeptidases, zinc-binding region signature.
Similarity search - Domain/homology
: / Angiotensin-converting enzyme
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsGregory, K.S. / Acharya, K.R. / Cozier, G.E.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)BB/X001032/1 United Kingdom
CitationJournal: Febs J. / Year: 2025
Title: Molecular basis of human angiotensin-1 converting enzyme inhibition by a series of diprolyl-derived compounds.
Authors: Gregory, K.S. / Cozier, G.E. / Fienberg, S. / Chibale, K. / Sturrock, E.D. / Acharya, K.R.
History
DepositionJul 31, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 22, 2025Provider: repository / Type: Initial release
Revision 1.1Mar 19, 2025Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Angiotensin-converting enzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,1926
Polymers68,8621
Non-polymers1,3305
Water2,846158
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1210 Å2
ΔGint-10 kcal/mol
Surface area24150 Å2
Unit cell
Length a, b, c (Å)56.821, 85.683, 135.12
Angle α, β, γ (deg.)90, 90, 90
Int Tables number19
Space group name H-MP212121

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Components

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Protein / Sugars , 2 types, 2 molecules A

#1: Protein Angiotensin-converting enzyme / ACE / Dipeptidyl carboxypeptidase I / Kininase II


Mass: 68861.875 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: g13-tACE / Source: (gene. exp.) Homo sapiens (human) / Gene: ACE, DCP, DCP1 / Production host: Cricetulus griseus (Chinese hamster)
References: UniProt: P12821, Hydrolases; Glycosylases; Glycosidases, i.e. enzymes that hydrolyse O- and S-glycosyl compounds, peptidyl-dipeptidase A
#2: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 732.682 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1221m-1a_1-5]/1-1-2-3/a4-b1_a6-d1_b4-c1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}[(6+1)][a-L-Fucp]{}}LINUCSPDB-CARE

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Non-polymers , 4 types, 162 molecules

#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-A1IJY / (2S)-1-[(2S)-2-[[(1S)-1-[(2S)-1-(4-carboxyphenyl)carbonylpyrrolidin-2-yl]-2-oxidanyl-2-oxidanylidene-ethyl]amino]propanoyl]pyrrolidine-2-carboxylic acid


Mass: 461.465 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H27N3O8 / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 158 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
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: 2.39 Å3/Da / Density % sol: 48.5 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, hanging drop / Details: 0.1 M MIB pH 4.0, 5% glycerol, and 15% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97625 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Oct 21, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 2.4→135.12 Å / Num. obs: 26594 / % possible obs: 100 % / Redundancy: 25.7 % / CC1/2: 0.994 / Rpim(I) all: 0.062 / Net I/σ(I): 8.4
Reflection shellResolution: 2.4→2.49 Å / Num. unique obs: 2750 / CC1/2: 0.841 / Rpim(I) all: 0.296

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→72.466 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.906 / WRfactor Rfree: 0.236 / WRfactor Rwork: 0.169 / SU B: 8.531 / SU ML: 0.197 / Average fsc free: 0.9554 / Average fsc work: 0.9779 / Cross valid method: FREE R-VALUE / ESU R: 0.415 / ESU R Free: 0.269 / Details: Hydrogens have not been used
RfactorNum. reflection% reflection
Rfree0.2487 1320 4.976 %
Rwork0.1784 25207 -
all0.182 --
obs-26527 99.955 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 35.814 Å2
Baniso -1Baniso -2Baniso -3
1--0.45 Å2-0 Å2-0 Å2
2---0.664 Å20 Å2
3---1.114 Å2
Refinement stepCycle: LAST / Resolution: 2.4→72.466 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4684 0 85 158 4927
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0124928
X-RAY DIFFRACTIONr_angle_refined_deg2.6531.8376709
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2245576
X-RAY DIFFRACTIONr_dihedral_angle_2_deg11.052526
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.22710805
X-RAY DIFFRACTIONr_dihedral_angle_6_deg15.50110240
X-RAY DIFFRACTIONr_chiral_restr0.1740.2714
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.023872
X-RAY DIFFRACTIONr_nbd_refined0.2340.22231
X-RAY DIFFRACTIONr_nbtor_refined0.3240.23342
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1650.2221
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.20.231
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1830.24
X-RAY DIFFRACTIONr_mcbond_it4.6583.362307
X-RAY DIFFRACTIONr_mcangle_it6.3746.0112882
X-RAY DIFFRACTIONr_scbond_it6.6153.7092621
X-RAY DIFFRACTIONr_scangle_it9.356.5823827
X-RAY DIFFRACTIONr_lrange_it10.16435.3767501
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
2.4-2.4620.2921100.22218330.22619440.9310.96799.94860.215
2.462-2.530.274810.1917750.19418570.9540.97699.94610.183
2.53-2.6030.242780.18717560.18918340.9610.9771000.177
2.603-2.6830.256910.19716880.217800.9580.97799.94380.185
2.683-2.7710.293810.21916380.22217200.9480.96999.94190.203
2.771-2.8680.313870.20115860.20716740.9370.97499.94030.185
2.868-2.9760.305730.19215410.19716140.940.9761000.177
2.976-3.0970.254970.1914510.19415480.9620.9771000.175
3.097-3.2350.313660.19814280.20314940.9370.9751000.187
3.235-3.3920.286770.213790.20514570.9480.97799.93140.188
3.392-3.5750.297710.19113000.19613730.9470.98199.85430.183
3.575-3.7920.197560.17112310.17212900.9740.98599.76740.165
3.792-4.0530.193590.14711670.14912260.9780.9871000.142
4.053-4.3760.229530.12910830.13411360.9680.991000.125
4.376-4.7920.203650.1279970.13110620.9790.9911000.123
4.792-5.3550.211550.1519180.1559730.9760.9881000.149
5.355-6.1780.235390.1828240.1858630.970.9841000.177
6.178-7.5520.21320.1617050.1637370.9770.9861000.159
7.552-10.6230.185300.1385630.145930.980.9881000.141
10.623-72.4660.302190.2783440.2793640.920.92899.72530.272

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