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- PDB-9ss7: Human angiotensin 1-converting enzyme C-domain in complex with re... -

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Basic information

Entry
Database: PDB / ID: 9ss7
TitleHuman angiotensin 1-converting enzyme C-domain in complex with rentiapril
ComponentsAngiotensin-converting enzyme, soluble form
KeywordsHYDROLASE / inhibitor / complex / metalloprotease
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 / metallodipeptidase activity / hormone catabolic process / bradykinin catabolic process / neutrophil mediated immunity / regulation of smooth muscle cell migration / regulation of hematopoietic stem cell proliferation / hormone metabolic process / mitogen-activated protein kinase kinase binding / mitogen-activated protein 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 / 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 / antigen processing and presentation of peptide antigen via MHC class I / 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 / metalloendopeptidase activity / regulation of synaptic plasticity / regulation of blood pressure / male gonad development / metallopeptidase activity / peptidase activity / actin binding / endopeptidase activity / spermatogenesis / 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
: / BORIC ACID / IMIDAZOLE / MALONATE ION / Angiotensin-converting enzyme
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 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: 2026
Title: Kinetic and structural characterisation of domain-specific angiotensin I-converting enzyme inhibition by captopril, rentiapril and zofenoprilat.
Authors: Gregory, K.S. / Ramasamy, V. / Sturrock, E.D. / Acharya, K.R.
History
DepositionSep 25, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 18, 2026Provider: 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)69,65113
Polymers67,5371
Non-polymers2,11412
Water3,189177
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)56.726, 84.945, 134.747
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: 67537.406 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 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: 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 , 8 types, 187 molecules

#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-A1JPY / Rentiapril / (2~{R},4~{R})-2-(2-hydroxyphenyl)-3-(3-sulfanylpropanoyl)-1,3-thiazolidine-4-carboxylic acid


Mass: 313.393 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C13H15NO4S2 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-MLI / MALONATE ION


Mass: 102.046 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H2O4
#7: Chemical ChemComp-BO3 / BORIC ACID


Mass: 61.833 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: BH3O3
#8: Chemical ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H5N2
#9: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#10: Chemical ChemComp-CL / CHLORIDE ION


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


Mass: 18.015 Da / Num. of mol.: 177 / 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: 2.42 Å3/Da / Density % sol: 49.07 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, hanging drop / pH: 4 / Details: 0.1 M MIB Buffer 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: 0.95373 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Apr 26, 2025
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95373 Å / Relative weight: 1
ReflectionResolution: 1.95→71.86 Å / Num. obs: 48340 / % possible obs: 100 % / Redundancy: 26.8 % / CC1/2: 0.997 / Rpim(I) all: 0.062 / Net I/σ(I): 9.8
Reflection shellResolution: 1.95→2 Å / Num. unique obs: 3334 / CC1/2: 0.42 / Rpim(I) all: 0.852

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Processing

Software
NameVersionClassification
REFMAC5.8.0431 (refmacat 0.4.105)refinement
xia2.multiplexdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.95→71.86 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.942 / SU B: 9.113 / SU ML: 0.123 / Cross valid method: THROUGHOUT / ESU R: 0.165 / ESU R Free: 0.147
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflectionSelection details
Rfree0.2229 2436 5.049 %RANDOM
Rwork0.1864 45812 --
all0.188 ---
obs-48248 99.954 %-
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: 33.536 Å2
Baniso -1Baniso -2Baniso -3
1--0.312 Å2-0 Å2-0 Å2
2---0.588 Å20 Å2
3---0.9 Å2
Refinement stepCycle: LAST / Resolution: 1.95→71.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4740 0 133 177 5050
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0125035
X-RAY DIFFRACTIONr_bond_other_d0.0010.0164565
X-RAY DIFFRACTIONr_angle_refined_deg1.6281.8246852
X-RAY DIFFRACTIONr_angle_other_deg0.5671.75910537
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1465582
X-RAY DIFFRACTIONr_dihedral_angle_2_deg7.774528
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.42810812
X-RAY DIFFRACTIONr_dihedral_angle_6_deg14.82110245
X-RAY DIFFRACTIONr_chiral_restr0.0810.2726
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.025928
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021200
X-RAY DIFFRACTIONr_nbd_refined0.2240.21086
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1840.24030
X-RAY DIFFRACTIONr_nbtor_refined0.1880.22466
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0760.22510
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1750.2176
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.240.216
X-RAY DIFFRACTIONr_nbd_other0.2190.252
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1970.213
X-RAY DIFFRACTIONr_mcbond_it1.8032.3062328
X-RAY DIFFRACTIONr_mcbond_other1.8032.3072329
X-RAY DIFFRACTIONr_mcangle_it2.6464.1372910
X-RAY DIFFRACTIONr_mcangle_other2.6474.1382911
X-RAY DIFFRACTIONr_scbond_it2.9512.7532707
X-RAY DIFFRACTIONr_scbond_other2.9512.7542708
X-RAY DIFFRACTIONr_scangle_it4.7214.913942
X-RAY DIFFRACTIONr_scangle_other4.724.9113943
X-RAY DIFFRACTIONr_lrange_it6.13125.0585772
X-RAY DIFFRACTIONr_lrange_other6.12224.8135740
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.95-2.0010.3221720.2973319X-RAY DIFFRACTION99.9141
2.001-2.0550.3091630.2763262X-RAY DIFFRACTION99.9416
2.055-2.1150.2721570.2543196X-RAY DIFFRACTION99.9106
2.115-2.180.2591780.2293079X-RAY DIFFRACTION100
2.18-2.2510.2671400.2182983X-RAY DIFFRACTION99.968
2.251-2.330.2471640.2012876X-RAY DIFFRACTION99.9671
2.33-2.4180.2531340.192818X-RAY DIFFRACTION99.9661
2.418-2.5170.2241520.1812678X-RAY DIFFRACTION99.9647
2.517-2.6290.2281530.1762578X-RAY DIFFRACTION99.9634
2.629-2.7570.2021280.1762492X-RAY DIFFRACTION99.9237
2.757-2.9060.2661330.1822342X-RAY DIFFRACTION100
2.906-3.0820.2351320.1812238X-RAY DIFFRACTION99.9578
3.082-3.2940.2821010.1852122X-RAY DIFFRACTION99.8652
3.557-3.8960.224870.1591818X-RAY DIFFRACTION100
3.896-4.3540.1811020.151660X-RAY DIFFRACTION100
4.354-5.0240.155950.1451460X-RAY DIFFRACTION100
5.024-6.1460.214680.1721278X-RAY DIFFRACTION100
6.146-8.6610.17430.1691009X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 12.2889 Å / Origin y: 5.6235 Å / Origin z: 23.9211 Å
111213212223313233
T0.0228 Å2-0.0168 Å20.0067 Å2-0.0275 Å20.0055 Å2--0.0117 Å2
L0.683 °2-0.0142 °20.0411 °2-0.8055 °20.3802 °2--0.883 °2
S-0.0388 Å °0.116 Å °0.0471 Å °-0.12 Å °0.0496 Å °-0.0757 Å °-0.0751 Å °0.0824 Å °-0.0108 Å °
Refinement TLS groupSelection: ALL

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