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- PDB-9qap: Human angiotensin-1 converting enzyme C-domain in complex with qu... -

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Basic information

Entry
Database: PDB / ID: 9qap
TitleHuman angiotensin-1 converting enzyme C-domain in complex with quinaprilat
ComponentsAngiotensin-converting enzyme, soluble form
KeywordsHYDROLASE / Inhibitor / complex / ACE / quinaprilat
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 / antigen processing and presentation of peptide antigen via MHC class I / positive regulation of systemic arterial blood pressure / 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 / regulation of vasoconstriction / peptidyl-dipeptidase activity / 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
: / BORIC ACID / IMIDAZOLE / DI(HYDROXYETHYL)ETHER / Angiotensin-converting enzyme
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsGregory, K.S. / Acharya, K.R.
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 domain-specific angiotensin I-converting enzyme inhibition by the antihypertensive drugs enalaprilat, ramiprilat, trandolaprilat, quinaprilat and perindoprilat.
Authors: Gregory, K.S. / Ramasamy, V. / Sturrock, E.D. / Acharya, K.R.
History
DepositionFeb 28, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 3, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Angiotensin-converting enzyme, soluble form
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,09317
Polymers66,7651
Non-polymers2,32816
Water10,953608
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3980 Å2
ΔGint-3 kcal/mol
Surface area23390 Å2
Unit cell
Length a, b, c (Å)59.72, 85.652, 135.73
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, soluble form


Mass: 66764.562 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ACE, DCP, DCP1 / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: P12821
#2: Polysaccharide alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)-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: 1056.964 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3DManpa1-6DManpb1-4DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/4,6,5/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5][a1221m-1a_1-5]/1-1-2-3-3-4/a4-b1_a6-f1_b4-c1_c6-d1_d3-e1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(6+1)][a-D-Manp]{[(3+1)][a-D-Manp]{}}}}[(6+1)][a-L-Fucp]{}}LINUCSPDB-CARE

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Non-polymers , 10 types, 623 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-A1I5A / quinaprilat / (3S)-2-[(2S)-2-[[(2S)-1-oxidanyl-1-oxidanylidene-4-phenyl-butan-2-yl]amino]propanoyl]-3,4-dihydro-1H-isoquinoline-3-carboxylic acid


Mass: 410.463 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H26N2O5 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H5N2
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#7: Chemical ChemComp-BO3 / BORIC ACID


Mass: 61.833 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: BH3O3
#8: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#9: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#10: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#11: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#12: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 608 / 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: 2.63 Å3/Da / Density % sol: 53.3 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, hanging drop / pH: 4 / Details: 0.1 M MIB pH 4.0, 5% glycerol, 15% PEG 3350.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.953701 Å
DetectorType: DECTRIS EIGER2 S 16M / Detector: PIXEL / Date: Sep 20, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.953701 Å / Relative weight: 1
ReflectionResolution: 1.5→135.73 Å / Num. obs: 112080 / % possible obs: 100 % / Redundancy: 13.2 % / CC1/2: 0.998 / Rmerge(I) obs: 0.138 / Rpim(I) all: 0.039 / Net I/σ(I): 9.5
Reflection shellResolution: 1.5→1.53 Å / Rmerge(I) obs: 2.137 / Num. unique obs: 5466 / CC1/2: 0.519 / Rpim(I) all: 0.605

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Processing

Software
NameVersionClassification
REFMAC5.8.0430 (refmacat 0.4.100)refinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.5→72.54 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.959 / SU B: 3.282 / SU ML: 0.051 / Cross valid method: FREE R-VALUE / ESU R: 0.068 / ESU R Free: 0.068
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1961 5625 5.023 %
Rwork0.1436 106355 -
all0.146 --
obs-111980 99.995 %
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: 25.587 Å2
Baniso -1Baniso -2Baniso -3
1-0.579 Å20 Å2-0 Å2
2---1.196 Å20 Å2
3---0.616 Å2
Refinement stepCycle: LAST / Resolution: 1.5→72.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4648 0 158 608 5414
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0125054
X-RAY DIFFRACTIONr_bond_other_d0.0010.0164614
X-RAY DIFFRACTIONr_angle_refined_deg2.0661.8296868
X-RAY DIFFRACTIONr_angle_other_deg0.7591.75910652
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0185590
X-RAY DIFFRACTIONr_dihedral_angle_2_deg9.937630
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.60210819
X-RAY DIFFRACTIONr_dihedral_angle_6_deg15.93910247
X-RAY DIFFRACTIONr_chiral_restr0.2430.2731
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.025954
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021208
X-RAY DIFFRACTIONr_nbd_refined0.2480.21122
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1910.24181
X-RAY DIFFRACTIONr_nbtor_refined0.1930.22509
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.080.22515
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1660.2439
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1490.220
X-RAY DIFFRACTIONr_nbd_other0.1870.230
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1740.222
X-RAY DIFFRACTIONr_mcbond_it7.682.1862336
X-RAY DIFFRACTIONr_mcbond_other7.6782.1862337
X-RAY DIFFRACTIONr_mcangle_it10.0483.9322934
X-RAY DIFFRACTIONr_mcangle_other10.0523.9332935
X-RAY DIFFRACTIONr_scbond_it11.9292.6492718
X-RAY DIFFRACTIONr_scbond_other11.9272.6492718
X-RAY DIFFRACTIONr_scangle_it16.1354.683934
X-RAY DIFFRACTIONr_scangle_other16.1334.6813935
X-RAY DIFFRACTIONr_lrange_it20.01625.5246104
X-RAY DIFFRACTIONr_lrange_other18.7824.2525925
X-RAY DIFFRACTIONr_rigid_bond_restr5.37739668
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
1.5-1.5390.3344230.31377560.31481790.8010.8011000.316
1.539-1.5810.3013730.26776130.26979870.9510.96399.98750.27
1.581-1.6270.2754030.22773470.2377500.9590.9741000.229
1.627-1.6770.2543940.19471580.19775530.9680.98199.98680.193
1.677-1.7320.2083500.16169540.16373040.9740.9871000.157
1.732-1.7930.2033640.14267440.14571090.9780.98999.98590.135
1.793-1.860.1813790.12565050.12868840.980.9911000.117
1.86-1.9360.1753340.1162530.11365870.9820.9931000.101
1.936-2.0220.1653250.11359910.11663170.9850.99399.98420.105
2.022-2.1210.2063140.12457550.12860700.9740.99399.98350.117
2.121-2.2350.1773030.1254670.12357700.9830.9931000.115
2.235-2.3710.1792820.11252190.11555020.9810.99499.98180.107
2.371-2.5340.1842470.1149020.11451490.9790.9941000.106
2.534-2.7370.1512360.10945890.11148250.9860.9931000.106
2.737-2.9980.1712170.11442470.11744640.9810.9921000.112
2.998-3.3510.1781840.1338470.13340310.9790.991000.129
3.351-3.8680.191800.13834150.14135950.9770.9891000.139
3.868-4.7340.1751470.1429160.14230630.9860.991000.142
4.734-6.6810.2631060.19323190.19624250.9820.9881000.196
6.681-72.540.25640.2413580.2414220.9670.9551000.239

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