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- PDB-9qao: Human angiotensin-1 converting enzyme C-domain in complex with tr... -

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Basic information

Entry
Database: PDB / ID: 9qao
TitleHuman angiotensin-1 converting enzyme C-domain in complex with trandolaprilat
ComponentsAngiotensin-converting enzyme, soluble form
KeywordsHYDROLASE / inhibitor / complex / hypertension / ACE / trandolaprilat
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
IMIDAZOLE / DI(HYDROXYETHYL)ETHER / TRANDOLAPRILAT / 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,9199
Polymers66,7651
Non-polymers2,1548
Water3,585199
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2830 Å2
ΔGint12 kcal/mol
Surface area24600 Å2
Unit cell
Length a, b, c (Å)57.036, 84.924, 134.306
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 , 1 types, 1 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

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Sugars , 2 types, 2 molecules

#2: Polysaccharide alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D- ...alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]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: 1219.105 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3DManpa1-6[DManpa1-3]DManpb1-4DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/4,7,6/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5][a1221m-1a_1-5]/1-1-2-3-3-3-4/a4-b1_a6-g1_b4-c1_c3-d1_c6-e1_e3-f1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{[(3+1)][a-D-Manp]{}}}}[(6+1)][a-L-Fucp]{}}LINUCSPDB-CARE
#5: 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 , 6 types, 205 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-X93 / TRANDOLAPRILAT


Mass: 402.484 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H30N2O5 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#7: Chemical ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H5N2
#8: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 199 / 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: 2.44 Å3/Da / Density % sol: 49.69 %
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: 0.953731 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 23, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.953731 Å / Relative weight: 1
ReflectionResolution: 2.3→134.31 Å / Num. obs: 29803 / % possible obs: 100 % / Redundancy: 13 % / CC1/2: 0.992 / Rmerge(I) obs: 0.316 / Rpim(I) all: 0.091 / Net I/σ(I): 6.6
Reflection shellResolution: 2.3→2.38 Å / Rmerge(I) obs: 1.617 / Num. unique obs: 2891 / CC1/2: 0.745 / Rpim(I) all: 0.664

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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→71.882 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.91 / SU B: 17.633 / SU ML: 0.209 / Cross valid method: FREE R-VALUE / ESU R: 0.346 / ESU R Free: 0.258
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2612 1508 5.073 %
Rwork0.1877 28216 -
all0.191 --
obs-29724 99.929 %
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: 34.525 Å2
Baniso -1Baniso -2Baniso -3
1-0.764 Å2-0 Å2-0 Å2
2---4.008 Å20 Å2
3---3.244 Å2
Refinement stepCycle: LAST / Resolution: 2.3→71.882 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4690 0 140 199 5029
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0124979
X-RAY DIFFRACTIONr_bond_other_d0.0010.0164536
X-RAY DIFFRACTIONr_angle_refined_deg2.2661.8256776
X-RAY DIFFRACTIONr_angle_other_deg0.7641.75710485
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1695573
X-RAY DIFFRACTIONr_dihedral_angle_2_deg8.9696.07128
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.86410804
X-RAY DIFFRACTIONr_dihedral_angle_6_deg14.70310241
X-RAY DIFFRACTIONr_chiral_restr0.1090.2734
X-RAY DIFFRACTIONr_gen_planes_refined0.010.025789
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021173
X-RAY DIFFRACTIONr_nbd_refined0.2420.21109
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1980.24132
X-RAY DIFFRACTIONr_nbtor_refined0.1980.22421
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0850.22540
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1750.2191
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1750.215
X-RAY DIFFRACTIONr_nbd_other0.2040.230
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.270.213
X-RAY DIFFRACTIONr_mcbond_it2.5282.1852298
X-RAY DIFFRACTIONr_mcbond_other2.5192.1862298
X-RAY DIFFRACTIONr_mcangle_it3.8173.9182869
X-RAY DIFFRACTIONr_mcangle_other3.8183.9192870
X-RAY DIFFRACTIONr_scbond_it3.6452.6352681
X-RAY DIFFRACTIONr_scbond_other3.6452.6382682
X-RAY DIFFRACTIONr_scangle_it5.644.73907
X-RAY DIFFRACTIONr_scangle_other5.644.7023908
X-RAY DIFFRACTIONr_lrange_it6.48522.9545706
X-RAY DIFFRACTIONr_lrange_other6.47822.8385673
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
2.3-2.360.3571130.29920650.30221780.9050.9271000.293
2.36-2.4240.303860.26419920.26620810.9230.94699.85580.257
2.424-2.4940.2961100.23919530.24220650.9380.95699.90310.231
2.494-2.5710.2731180.20618730.2119930.940.97299.89970.194
2.571-2.6550.299980.21918260.22319240.9440.9681000.207
2.655-2.7480.337810.22717990.23118810.9270.96199.94680.21
2.748-2.8520.2921000.20717250.21118270.9480.97299.89050.191
2.852-2.9680.283770.19416560.19817340.9590.97699.94230.177
2.968-3.10.283650.17916140.18316790.9490.981000.164
3.1-3.2510.239820.17615080.17915930.9650.98299.81170.162
3.251-3.4260.275750.18514600.18915360.9520.9899.93490.17
3.426-3.6340.29700.1913850.19514560.9580.97999.93130.175
3.634-3.8840.259890.16412930.1713830.9670.98199.92770.15
3.884-4.1940.195650.15412120.15612780.9760.98699.92180.145
4.194-4.5930.213750.13811090.14311850.9750.9999.91560.131
4.593-5.1320.222490.13110440.13410940.9810.99199.90860.126
5.132-5.9210.214540.1629010.1659550.9760.9861000.155
5.921-7.240.297480.1827940.1898420.9520.9791000.174
7.24-10.1870.187390.1386160.1416550.9780.9881000.141
10.187-71.8820.269140.2413910.2424060.9570.94999.75370.252
Refinement TLS params.Method: refined / Origin x: 12.7473 Å / Origin y: 5.2375 Å / Origin z: 23.3377 Å
111213212223313233
T0.0198 Å2-0.0144 Å20.0099 Å2-0.0346 Å20.0092 Å2--0.0165 Å2
L0.9797 °2-0.0612 °2-0.1175 °2-1.0278 °20.5981 °2--1.1054 °2
S-0.0436 Å °0.1623 Å °0.056 Å °-0.1325 Å °0.0443 Å °-0.0971 Å °-0.0725 Å °0.0724 Å °-0.0007 Å °
Refinement TLS groupSelection: ALL

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