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- PDB-9qav: Human angiotensin-1 converting enzyme N-domain in complex with en... -

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Basic information

Entry
Database: PDB / ID: 9qav
TitleHuman angiotensin-1 converting enzyme N-domain in complex with enalaprilat
ComponentsAngiotensin-converting enzyme, soluble form
KeywordsHYDROLASE / Inhibitor / complex / enalaprilat / hypertension
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
Chem-EAL / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / Angiotensin-converting enzyme
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 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)145,78330
Polymers140,7322
Non-polymers5,05128
Water3,135174
1
A: Angiotensin-converting enzyme, soluble form
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,21615
Polymers70,3661
Non-polymers2,85014
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Angiotensin-converting enzyme, soluble form
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,56715
Polymers70,3661
Non-polymers2,20114
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)72.281, 77.586, 80.996
Angle α, β, γ (deg.)88.714, 64.857, 75.072
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: LEU / Beg label comp-ID: LEU / End auth comp-ID: TYR / End label comp-ID: TYR / Auth seq-ID: 1 - 607 / Label seq-ID: 1 - 607

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 , 3 types, 6 molecules

#2: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 570.542 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-1-2/a4-b1_a6-c1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}[(6+1)][a-L-Fucp]{}}LINUCSPDB-CARE
#3: 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.: 2
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
#11: 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: 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 , 9 types, 196 molecules

#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#6: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H10O3
#7: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


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


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#9: Chemical ChemComp-EAL / 1-((2S)-2-{[(1S)-1-CARBOXY-3-PHENYLPROPYL]AMINO}PROPANOYL)-L-PROLINE / ENALAPRILAT INHIBITOR


Mass: 348.394 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C18H24N2O5 / Feature type: SUBJECT OF INVESTIGATION
#10: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#12: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#13: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 174 / 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: 2.83 Å3/Da / Density % sol: 56.57 %
Crystal growTemperature: 289 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: 0.953731 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 8, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.953731 Å / Relative weight: 1
ReflectionResolution: 2.3→74.6 Å / Num. obs: 67085 / % possible obs: 98.6 % / Redundancy: 3.6 % / CC1/2: 0.987 / Rpim(I) all: 0.1 / Net I/σ(I): 5.4
Reflection shellResolution: 2.3→2.35 Å / Num. unique obs: 4510 / CC1/2: 0.412 / Rpim(I) all: 0.784

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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: 2.3→74.595 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.932 / WRfactor Rfree: 0.208 / WRfactor Rwork: 0.163 / SU B: 18.326 / SU ML: 0.197 / Average fsc free: 0.9586 / Average fsc work: 0.9706 / Cross valid method: FREE R-VALUE / ESU R: 0.285 / ESU R Free: 0.212
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2238 3309 4.935 %
Rwork0.1772 63739 -
all0.179 --
obs-67048 98.529 %
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: 39.947 Å2
Baniso -1Baniso -2Baniso -3
1--0.357 Å20.634 Å20.451 Å2
2---0.649 Å2-0.668 Å2
3---1.479 Å2
Refinement stepCycle: LAST / Resolution: 2.3→74.595 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9869 0 326 174 10369
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.01210524
X-RAY DIFFRACTIONr_bond_other_d0.0010.0169480
X-RAY DIFFRACTIONr_angle_refined_deg2.0571.8214301
X-RAY DIFFRACTIONr_angle_other_deg0.6821.74921867
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.95951205
X-RAY DIFFRACTIONr_dihedral_angle_2_deg10.031568
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.79101603
X-RAY DIFFRACTIONr_dihedral_angle_6_deg15.09310529
X-RAY DIFFRACTIONr_chiral_restr0.0940.21492
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0212456
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022584
X-RAY DIFFRACTIONr_nbd_refined0.2270.22499
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1920.29180
X-RAY DIFFRACTIONr_nbtor_refined0.1950.25227
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0880.25500
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1660.2318
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0410.22
X-RAY DIFFRACTIONr_metal_ion_refined00.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2440.212
X-RAY DIFFRACTIONr_nbd_other0.2160.276
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2510.24
X-RAY DIFFRACTIONr_mcbond_it2.3962.4164831
X-RAY DIFFRACTIONr_mcbond_other2.3592.4144829
X-RAY DIFFRACTIONr_mcangle_it3.5344.336031
X-RAY DIFFRACTIONr_mcangle_other3.5344.3316032
X-RAY DIFFRACTIONr_scbond_it3.6342.8455693
X-RAY DIFFRACTIONr_scbond_other3.6342.8465694
X-RAY DIFFRACTIONr_scangle_it5.4315.0578270
X-RAY DIFFRACTIONr_scangle_other5.4315.0588271
X-RAY DIFFRACTIONr_lrange_it6.44224.35612193
X-RAY DIFFRACTIONr_lrange_other6.44224.35412179
X-RAY DIFFRACTIONr_ncsr_local_group_10.0970.0521282
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AX-RAY DIFFRACTIONLocal ncs0.096820.05008
12BX-RAY DIFFRACTIONLocal ncs0.096820.05008
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
2.3-2.360.2942400.28946960.28950590.9350.93797.56870.293
2.36-2.4240.2942530.28645350.28748940.9380.94197.83410.289
2.424-2.4940.3192510.2843980.28247510.9320.94597.85310.281
2.494-2.5710.2862030.25243150.25446110.9430.95697.98310.251
2.571-2.6550.2761980.24142210.24245020.9510.96398.15640.239
2.655-2.7480.2952250.23640620.23943650.9440.96798.21310.232
2.748-2.8520.2432200.20338820.20541720.9640.97698.32210.196
2.852-2.9680.2352060.18837780.1940420.9650.97998.56510.179
2.968-3.10.2341800.18536230.18838570.9620.97998.59990.174
3.1-3.2510.2351740.1834810.18237030.9660.98198.70380.169
3.251-3.4270.2281470.16533270.16735140.9650.98598.86170.154
3.427-3.6340.2021620.15431290.15633240.9780.98799.00720.145
3.634-3.8840.171630.13329420.13531350.9840.99199.04310.126
3.884-4.1950.1821480.13127300.13429010.9790.9999.20720.124
4.195-4.5930.1761180.12525490.12826860.980.99199.29260.118
4.593-5.1330.1731160.11622870.11924170.9850.99399.42080.11
5.133-5.9230.2061010.16120270.16321390.9750.98899.48570.153
5.923-7.2420.257960.17316980.17818040.9640.98499.44570.166
7.242-10.1940.161740.13213220.13414000.9850.9999.71430.13
10.194-74.5950.255340.2077370.2097730.9750.97499.74130.207
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)
11.21630.15810.06041.21810.20910.63590.04340.0238-0.0466-0.04470.0163-0.0393-0.00060.0135-0.05970.07630.03680.02130.0210.00650.01671.2135-14.5376-19.1309
20.8285-0.2769-0.16681.0222-0.11021.5235-0.0399-0.0783-0.04410.11640.04590.11080.0064-0.0806-0.0060.08830.01220.0490.0348-0.02720.0962-2.755215.5917.7879
Refinement TLS group
IDRefine-IDRefine TLS-IDSelectionAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1ALLA1 - 711
2X-RAY DIFFRACTION2ALLB1 - 711

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