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- PDB-9qat: Human angiotensin-1 converting enzyme N-domain in complex with qu... -

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Basic information

Entry
Database: PDB / ID: 9qat
TitleHuman angiotensin-1 converting enzyme N-domain in complex with quinaprilat
ComponentsAngiotensin-converting enzyme, soluble form
KeywordsHYDROLASE / Inhibitor / complex / quinaprilat / 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 / 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
: / ACETATE ION / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / 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)146,48834
Polymers140,7322
Non-polymers5,75532
Water9,890549
1
A: Angiotensin-converting enzyme, soluble form
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,70721
Polymers70,3661
Non-polymers3,34120
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Angiotensin-converting enzyme, soluble form
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,78013
Polymers70,3661
Non-polymers2,41412
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)72.84, 77.997, 81.707
Angle α, β, γ (deg.)88.451, 64.62, 74.697
Int Tables number1
Space group name H-MP1

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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 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
#4: 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
#5: 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.: 1
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
#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 , 12 types, 575 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-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#8: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C4H10O3
#9: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#10: 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.: 2 / Source method: obtained synthetically / Formula: C23H26N2O5 / Feature type: SUBJECT OF INVESTIGATION
#11: Chemical ChemComp-P6G / HEXAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400


Mass: 282.331 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H26O7 / Comment: precipitant*YM
#12: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H3O2
#13: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#14: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


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


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#17: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#18: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 549 / 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: 2.89 Å3/Da / Density % sol: 57.39 %
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: 0.929813 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 29, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.929813 Å / Relative weight: 1
ReflectionResolution: 2.2→74.863 Å / Num. obs: 78017 / % possible obs: 98.5 % / Redundancy: 3.5 % / CC1/2: 0.991 / Rpim(I) all: 0.052 / Net I/σ(I): 9.1
Reflection shellResolution: 2.2→2.24 Å / Num. unique obs: 4410 / CC1/2: 0.87 / Rpim(I) all: 0.256

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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→74.863 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.941 / SU B: 5.242 / SU ML: 0.131 / Cross valid method: FREE R-VALUE / ESU R: 0.222 / ESU R Free: 0.181
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2101 3864 4.954 %
Rwork0.1663 74132 -
all0.168 --
obs-77996 98.505 %
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: 30.408 Å2
Baniso -1Baniso -2Baniso -3
1--0.097 Å21.512 Å21.282 Å2
2---0.046 Å2-0.492 Å2
3---1.672 Å2
Refinement stepCycle: LAST / Resolution: 2.2→74.863 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9861 0 375 549 10785
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.01210633
X-RAY DIFFRACTIONr_bond_other_d0.0010.0169549
X-RAY DIFFRACTIONr_angle_refined_deg1.6731.81914452
X-RAY DIFFRACTIONr_angle_other_deg0.5941.74922028
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.67251218
X-RAY DIFFRACTIONr_dihedral_angle_2_deg8.4245.84571
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.477101611
X-RAY DIFFRACTIONr_dihedral_angle_6_deg14.73310533
X-RAY DIFFRACTIONr_chiral_restr0.0840.21508
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0212597
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022611
X-RAY DIFFRACTIONr_nbd_refined0.2290.22428
X-RAY DIFFRACTIONr_symmetry_nbd_other0.190.28773
X-RAY DIFFRACTIONr_nbtor_refined0.1910.25205
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0810.25245
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1770.2555
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0510.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1070.217
X-RAY DIFFRACTIONr_nbd_other0.2160.260
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1880.210
X-RAY DIFFRACTIONr_mcbond_it2.692.84867
X-RAY DIFFRACTIONr_mcbond_other2.6872.7994863
X-RAY DIFFRACTIONr_mcangle_it3.9615.0176082
X-RAY DIFFRACTIONr_mcangle_other3.9615.0186083
X-RAY DIFFRACTIONr_scbond_it3.3983.2235766
X-RAY DIFFRACTIONr_scbond_other3.3983.2245767
X-RAY DIFFRACTIONr_scangle_it5.4025.7478370
X-RAY DIFFRACTIONr_scangle_other5.4025.7478371
X-RAY DIFFRACTIONr_lrange_it6.90128.47312425
X-RAY DIFFRACTIONr_lrange_other6.8928.32912314
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
2.2-2.2570.2692730.22354400.22558470.9520.96197.70820.215
2.257-2.3190.2483020.21552910.21757230.9580.96897.72850.207
2.319-2.3860.2312760.19951460.20155410.9630.97397.85240.191
2.386-2.4590.2482630.19349970.19553670.9620.97698.00630.184
2.459-2.540.2472670.17748840.1852520.9660.9898.07690.166
2.54-2.6290.2242290.17547020.17750230.9680.98298.16840.163
2.629-2.7280.2192310.17945880.18149000.9690.98198.34690.167
2.728-2.8390.2282380.16843610.17146730.9680.98398.41640.157
2.839-2.9650.2342070.17342490.17645130.9710.98298.7370.163
2.965-3.110.2132020.16840410.1742990.9730.98398.69740.158
3.11-3.2780.1921960.16838720.16941180.9770.98498.78580.161
3.278-3.4760.2171840.1736250.17238560.9730.98598.78110.166
3.476-3.7160.1981980.15834050.16136410.9760.98698.95630.156
3.716-4.0130.1981580.13931820.14133760.9770.98998.93360.138
4.013-4.3940.181400.13929600.14131160.980.98899.48650.141
4.394-4.9110.1861420.14226510.14428140.9820.98999.25370.145
4.911-5.6670.1971190.1523610.15224920.9810.98999.51850.153
5.667-6.930.2311020.17319830.17520930.9770.98599.61780.175
6.93-9.7590.164920.13615280.13716240.9840.98999.75370.141
9.759-74.8630.159450.198660.1899120.9850.97699.89040.198

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