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- PDB-9qas: Human angiotensin-1 converting enzyme N-domain in complex with tr... -

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Basic information

Entry
Database: PDB / ID: 9qas
TitleHuman angiotensin-1 converting enzyme N-domain in complex with trandolaprilat
ComponentsAngiotensin-converting enzyme, soluble form
KeywordsHYDROLASE / inhibitor / complex / trandolaprilat / 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 / 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
ACETATE ION / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / TRANDOLAPRILAT / Angiotensin-converting enzyme
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 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)146,11331
Polymers140,7322
Non-polymers5,38129
Water13,097727
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10930 Å2
ΔGint26 kcal/mol
Surface area45730 Å2
Unit cell
Length a, b, c (Å)73.18, 77.6, 82.461
Angle α, β, γ (deg.)88.469, 64.397, 74.767
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 , 4 types, 5 molecules

#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
#3: 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
#4: 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
#5: Polysaccharide alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 367.349 Da / Num. of mol.: 1
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

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Non-polymers , 10 types, 751 molecules

#6: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#7: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#8: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C4H10O3
#9: Chemical ChemComp-X93 / TRANDOLAPRILAT


Mass: 402.484 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C22H30N2O5 / Feature type: SUBJECT OF INVESTIGATION
#10: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#11: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O4
#12: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#13: Chemical ChemComp-CL / CHLORIDE ION


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


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#15: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 727 / 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: 2.9 Å3/Da / Density % sol: 57.65 %
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: I24 / Wavelength: 0.619914 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 1, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.619914 Å / Relative weight: 1
ReflectionResolution: 2.2→74.5 Å / Num. obs: 79191 / % possible obs: 99.3 % / Redundancy: 3.4 % / CC1/2: 0.996 / Rmerge(I) obs: 0.057 / Rpim(I) all: 0.036 / Net I/σ(I): 12.4
Reflection shellResolution: 2.2→2.24 Å / Num. unique obs: 4493 / CC1/2: 0.959 / Rpim(I) all: 0.129

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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: 2.2→74.103 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.937 / SU B: 9.679 / SU ML: 0.131 / Cross valid method: FREE R-VALUE / ESU R: 0.225 / ESU R Free: 0.183
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2126 3922 4.953 %
Rwork0.1687 75255 -
all0.171 --
obs-79177 99.265 %
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: 32.428 Å2
Baniso -1Baniso -2Baniso -3
1--0.284 Å21.745 Å20.859 Å2
2--0.992 Å2-0.63 Å2
3---0.847 Å2
Refinement stepCycle: LAST / Resolution: 2.2→74.103 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9869 0 347 727 10943
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.01210650
X-RAY DIFFRACTIONr_bond_other_d0.0010.0169570
X-RAY DIFFRACTIONr_angle_refined_deg2.2231.81814482
X-RAY DIFFRACTIONr_angle_other_deg0.7621.74822083
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.76151227
X-RAY DIFFRACTIONr_dihedral_angle_2_deg10.5355.85770
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.254101619
X-RAY DIFFRACTIONr_dihedral_angle_6_deg14.75310532
X-RAY DIFFRACTIONr_chiral_restr0.1110.21519
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0212621
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022607
X-RAY DIFFRACTIONr_nbd_refined0.2350.22510
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1940.28940
X-RAY DIFFRACTIONr_nbtor_refined0.1960.25202
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0880.25441
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1930.2675
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0370.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1790.213
X-RAY DIFFRACTIONr_nbd_other0.1990.263
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1680.29
X-RAY DIFFRACTIONr_mcbond_it1.8951.4134893
X-RAY DIFFRACTIONr_mcbond_other1.7941.4094885
X-RAY DIFFRACTIONr_mcangle_it2.7292.5196119
X-RAY DIFFRACTIONr_mcangle_other2.7292.5196120
X-RAY DIFFRACTIONr_scbond_it2.9421.7975757
X-RAY DIFFRACTIONr_scbond_other2.9421.7985758
X-RAY DIFFRACTIONr_scangle_it4.3763.1638363
X-RAY DIFFRACTIONr_scangle_other4.3763.1648364
X-RAY DIFFRACTIONr_lrange_it6.18215.29712627
X-RAY DIFFRACTIONr_lrange_other6.14814.96412440
X-RAY DIFFRACTIONr_ncsr_local_group_10.1150.0521068
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AX-RAY DIFFRACTIONLocal ncs0.115350.05007
12BX-RAY DIFFRACTIONLocal ncs0.115350.05007
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
2.2-2.2570.2772700.20855890.21159220.9520.97298.93620.199
2.257-2.3190.2513210.20153360.20457150.9630.97498.98510.192
2.319-2.3860.2242730.19252630.19355970.9670.97798.91010.183
2.386-2.4590.2322670.17950940.18154090.9680.9899.11260.171
2.459-2.540.2532710.17749920.18153160.960.98199.0030.171
2.54-2.6290.2432490.17747720.18150600.9670.98199.22920.171
2.629-2.7280.2342210.18946820.19149460.9650.97999.13060.185
2.728-2.8390.2512490.1844070.18346880.9610.9899.31740.178
2.839-2.9650.2172070.18343190.18445580.970.9899.29790.181
2.965-3.110.2292110.17340590.17543000.9670.98299.30230.174
3.11-3.2780.211970.18339290.18541480.9740.98199.46960.186
3.278-3.4760.221850.18337100.18539150.9720.98399.48910.189
3.476-3.7160.2221980.17334240.17536430.9730.98499.42360.18
3.716-4.0130.191540.14632390.14834060.9780.98899.61830.157
4.013-4.3940.1821430.13929750.14131360.9790.98899.4260.155
4.394-4.9110.1781420.13826750.1428290.9840.9999.57580.153
4.911-5.6660.1561210.13623910.13725180.9880.99199.76170.152
5.666-6.930.2041060.16319970.16521070.980.98799.81020.179
6.93-9.7570.19930.13715330.1416300.980.98999.75460.161
9.757-74.1030.147440.1968700.1949200.990.97899.34780.285
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)
11.3333-0.24860.12941.32520.27060.56960.08270.1155-0.0976-0.0931-0.05940.07360.0060.0054-0.02330.0149-0.0067-0.01450.07010.00490.01491.6782-14.8186-19.101
21.1548-0.4397-0.45121.66540.67562.0382-0.0907-0.1879-0.08250.22270.0730.08050.1289-0.01820.01770.0775-0.0093-0.00390.0736-0.0020.0592-1.968115.104318.3663
Refinement TLS group
IDRefine-IDRefine TLS-IDSelectionAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1ALLAp1 - 711
2X-RAY DIFFRACTION2ALLBp1 - 709

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