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- PDB-9qar: Human angiotensin-1 converting enzyme N-domain in complex with ra... -

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Basic information

Entry
Database: PDB / ID: 9qar
TitleHuman angiotensin-1 converting enzyme N-domain in complex with ramiprilat
ComponentsAngiotensin-converting enzyme, soluble form
KeywordsHYDROLASE / inhibitor / complex / ramiprilat / zinc
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 / 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
ACETATE ION / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / RAMIPRILAT / Angiotensin-converting enzyme
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 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
B: Angiotensin-converting enzyme, soluble form
hetero molecules


Theoretical massNumber of molelcules
Total (without water)146,02331
Polymers140,7322
Non-polymers5,29129
Water14,070781
1
A: Angiotensin-converting enzyme, soluble form
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,20217
Polymers70,3661
Non-polymers2,83616
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Angiotensin-converting enzyme, soluble form
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,82114
Polymers70,3661
Non-polymers2,45513
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)73.284, 77.814, 83.43
Angle α, β, γ (deg.)88.383, 63.983, 74.549
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: ASP / Beg label comp-ID: ASP / End auth comp-ID: PRO / End label comp-ID: PRO / Auth seq-ID: 2 - 608 / Label seq-ID: 2 - 608

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

NCS ensembles : (Details: Local NCS retraints between domains: 1 2)

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Angiotensin-converting enzyme, soluble form


Mass: 70366.094 Da / Num. of mol.: 2
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

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Sugars , 5 types, 6 molecules

#2: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE
#3: Polysaccharide alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 367.349 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
LFucpa1-6DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-2/a6-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(6+1)][a-L-Fucp]{}}LINUCSPDB-CARE
#4: 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
#5: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}LINUCSPDB-CARE
#15: 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.: 1 / 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

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Non-polymers , 11 types, 804 molecules

#6: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical ChemComp-X92 / Ramiprilat


Mass: 388.457 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H28N2O5 / Feature type: SUBJECT OF INVESTIGATION
#8: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H14O4
#9: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#10: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#11: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#12: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#13: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#14: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#16: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#17: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 781 / 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: 2.94 Å3/Da / Density % sol: 58.12 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.1 M Tris/Bicine pH 8.5, 0.06 M Divalent Cations, 30% PEG550MME/PEG20000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.953738 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 17, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.953738 Å / Relative weight: 1
ReflectionResolution: 2→74.61 Å / Num. obs: 105349 / % possible obs: 98.1 % / Redundancy: 3.5 % / CC1/2: 0.998 / Rpim(I) all: 0.024 / Net I/σ(I): 18.6
Reflection shellResolution: 2→2.03 Å / Num. unique obs: 5271 / Rpim(I) all: 0.094

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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: 2→74.608 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.938 / SU B: 7.216 / SU ML: 0.105 / Cross valid method: FREE R-VALUE / ESU R: 0.162 / ESU R Free: 0.145
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2123 5267 5 %
Rwork0.1771 100079 -
all0.179 --
obs-105346 98.142 %
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: 32.886 Å2
Baniso -1Baniso -2Baniso -3
1-0.276 Å21.111 Å20.451 Å2
2--0.563 Å2-0.387 Å2
3---0.231 Å2
Refinement stepCycle: LAST / Resolution: 2→74.608 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9870 0 342 781 10993
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.01210658
X-RAY DIFFRACTIONr_bond_other_d0.0010.0169582
X-RAY DIFFRACTIONr_angle_refined_deg1.8821.8214502
X-RAY DIFFRACTIONr_angle_other_deg0.6821.75122099
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.43651227
X-RAY DIFFRACTIONr_dihedral_angle_2_deg9.925.83372
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.292101624
X-RAY DIFFRACTIONr_dihedral_angle_6_deg15.42610539
X-RAY DIFFRACTIONr_chiral_restr0.2530.21517
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0212678
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022630
X-RAY DIFFRACTIONr_nbd_refined0.230.22411
X-RAY DIFFRACTIONr_symmetry_nbd_other0.190.28795
X-RAY DIFFRACTIONr_nbtor_refined0.1910.25232
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0830.25221
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1880.2667
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0790.22
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2220.212
X-RAY DIFFRACTIONr_nbd_other0.2360.259
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1330.29
X-RAY DIFFRACTIONr_mcbond_it1.6191.3824888
X-RAY DIFFRACTIONr_mcbond_other1.6141.3814885
X-RAY DIFFRACTIONr_mcangle_it2.4492.4726119
X-RAY DIFFRACTIONr_mcangle_other2.4492.4736120
X-RAY DIFFRACTIONr_scbond_it2.5231.7395770
X-RAY DIFFRACTIONr_scbond_other2.5231.7395771
X-RAY DIFFRACTIONr_scangle_it3.8453.0748383
X-RAY DIFFRACTIONr_scangle_other3.8443.0758384
X-RAY DIFFRACTIONr_lrange_it5.7714.96712545
X-RAY DIFFRACTIONr_lrange_other5.7714.96612543
X-RAY DIFFRACTIONr_ncsr_local_group_10.10.0521274
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AX-RAY DIFFRACTIONLocal ncs0.099810.05008
12BX-RAY DIFFRACTIONLocal ncs0.099810.05008
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
2-2.0520.2723550.22373570.22679460.9530.96997.05510.209
2.052-2.1080.243700.2171310.21177260.9650.97197.08780.196
2.108-2.1690.2613600.21169620.21475230.9580.97297.32820.197
2.169-2.2360.233660.267670.20173110.9660.97497.56530.189
2.236-2.3090.2393520.19965730.20170940.9620.97497.61770.189
2.309-2.390.2313220.19563850.19768620.9670.97697.74120.188
2.39-2.480.2233310.18861050.1965720.9690.97897.93060.183
2.48-2.5810.2233510.1858950.18363670.9680.97998.09960.177
2.581-2.6960.2283130.18657200.18861440.9660.97998.19340.184
2.696-2.8270.2133070.18254090.18458080.9690.9898.4160.182
2.827-2.980.2392550.18552220.18855550.9660.97998.59590.188
2.98-3.1610.2222700.18148870.18352280.9690.98198.64190.185
3.161-3.3780.2032310.18146550.18249420.9750.98298.86690.187
3.378-3.6480.2012120.18343400.18446010.9760.98298.9350.19
3.648-3.9960.192090.15539400.15741870.980.98799.09240.168
3.996-4.4660.1721760.1436350.14238410.9830.98899.2190.156
4.466-5.1540.181590.14131890.14333680.9820.9999.40620.158
5.154-6.3040.1851590.15726570.15828300.9830.98999.50530.171
6.304-8.8840.181180.15120830.15322090.9810.98899.63780.175
8.884-74.6080.262510.20911650.21112240.9530.97199.34640.306
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)
11.156-0.1510.15021.15550.21490.55690.04320.113-0.0794-0.0784-0.02290.01370.01250.0454-0.02030.00750.0025-0.00530.10530.01970.01640.7018-14.4057-19.449
21.1351-0.3476-0.39931.63830.85241.9029-0.0946-0.19190.01170.35470.08980.08680.20510.01120.00480.1213-0.00130.01370.1017-0.00140.0788-2.287415.574818.3208
Refinement TLS group
IDRefine-IDRefine TLS-IDSelectionAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1ALLA1 - 709
2X-RAY DIFFRACTION2ALLB2 - 709

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