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- PDB-9ss9: Human angiotensin 1-converting enzyme N-domain in complex with ca... -

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Basic information

Entry
Database: PDB / ID: 9ss9
TitleHuman angiotensin 1-converting enzyme N-domain in complex with captopril
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
Chem-MCO / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / L-CAPTOPRIL / Angiotensin-converting enzyme
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 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
B: Angiotensin-converting enzyme, soluble form
A: Angiotensin-converting enzyme, soluble form
hetero molecules


Theoretical massNumber of molelcules
Total (without water)148,81926
Polymers144,9872
Non-polymers3,83324
Water1,24369
1
B: Angiotensin-converting enzyme, soluble form
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,53113
Polymers72,4931
Non-polymers2,03812
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Angiotensin-converting enzyme, soluble form
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,28813
Polymers72,4931
Non-polymers1,79512
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)72.043, 77.499, 80.628
Angle α, β, γ (deg.)89.305, 65.326, 75.336
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11B
21A

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: ASP / Beg label comp-ID: ASP / End auth comp-ID: PRO / End label comp-ID: PRO / Auth seq-ID: 2 - 608 / Label seq-ID: 2 - 608

Dom-IDAuth asym-IDLabel asym-ID
1BA
2AB

NCS ensembles : (Details: Local NCS retraints between domains: 1 2)

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Components

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Protein , 1 types, 2 molecules BA

#1: Protein Angiotensin-converting enzyme, soluble form


Mass: 72493.352 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 , 2 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.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam 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
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#9: 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.: 4 / 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 , 10 types, 87 molecules

#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O4
#7: Chemical ChemComp-BCN / BICINE


Mass: 163.172 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4 / Comment: pH buffer*YM
#8: Chemical ChemComp-X8Z / L-CAPTOPRIL


Mass: 217.285 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H15NO3S / Comment: inhibitor, medication*YM
#10: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#11: Chemical ChemComp-MCO / 1-(3-MERCAPTO-2-METHYL-PROPIONYL)-PYRROLIDINE-2-CARBOXYLIC ACID


Mass: 217.285 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H15NO3S / Feature type: SUBJECT OF INVESTIGATION
#12: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#13: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 69 / 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: 56.48 %
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: 0.9537 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Apr 25, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.5→74.55 Å / Num. obs: 52092 / % possible obs: 98.8 % / Redundancy: 7 % / CC1/2: 0.993 / Rpim(I) all: 0.084 / Net I/σ(I): 6.2
Reflection shellResolution: 2.5→2.58 Å / Redundancy: 6.9 % / Mean I/σ(I) obs: 1.2 / Num. unique obs: 4517 / CC1/2: 0.645 / Rpim(I) all: 0.605

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Processing

Software
NameVersionClassification
REFMAC5.8.0431 (refmacat 0.4.105)refinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→74.549 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.935 / SU B: 24.512 / SU ML: 0.242 / Cross valid method: THROUGHOUT / ESU R: 0.505 / ESU R Free: 0.262
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflectionSelection details
Rfree0.2268 2569 4.932 %RANDOM
Rwork0.1848 49519 --
all0.187 ---
obs-52088 98.803 %-
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: 44.868 Å2
Baniso -1Baniso -2Baniso -3
1--1.367 Å20.035 Å23.003 Å2
2--2.266 Å21.559 Å2
3---0.674 Å2
Refinement stepCycle: LAST / Resolution: 2.5→74.549 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9844 0 241 69 10154
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.01210408
X-RAY DIFFRACTIONr_bond_other_d0.0010.0169387
X-RAY DIFFRACTIONr_angle_refined_deg1.631.81714150
X-RAY DIFFRACTIONr_angle_other_deg0.5511.75121637
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.66951202
X-RAY DIFFRACTIONr_dihedral_angle_2_deg10.1375.43569
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.8101597
X-RAY DIFFRACTIONr_dihedral_angle_6_deg14.68910528
X-RAY DIFFRACTIONr_chiral_restr0.0760.21466
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0212398
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022570
X-RAY DIFFRACTIONr_nbd_refined0.2240.22377
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1920.28952
X-RAY DIFFRACTIONr_nbtor_refined0.1920.25130
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0810.25368
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1870.2183
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0760.23
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1480.222
X-RAY DIFFRACTIONr_nbd_other0.2150.274
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.120.24
X-RAY DIFFRACTIONr_mcbond_it2.2992.824817
X-RAY DIFFRACTIONr_mcbond_other2.2982.824817
X-RAY DIFFRACTIONr_mcangle_it3.5435.0666016
X-RAY DIFFRACTIONr_mcangle_other3.5435.0676017
X-RAY DIFFRACTIONr_scbond_it3.1833.2015591
X-RAY DIFFRACTIONr_scbond_other3.1833.2025592
X-RAY DIFFRACTIONr_scangle_it4.9995.7228134
X-RAY DIFFRACTIONr_scangle_other4.9995.7238135
X-RAY DIFFRACTIONr_lrange_it6.30828.65411864
X-RAY DIFFRACTIONr_lrange_other6.30928.65511859
X-RAY DIFFRACTIONr_ncsr_local_group_10.0740.0521591
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11BX-RAY DIFFRACTIONLocal ncs0.073730.05009
12AX-RAY DIFFRACTIONLocal ncs0.073730.05009
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
2.5-2.5650.2971870.27235820.27338430.9320.94398.07440.276
2.565-2.6350.3011880.27435690.27538230.9390.94398.27360.277
2.635-2.7110.3281700.25734580.2636930.9350.95398.23990.255
2.711-2.7950.2841690.25233810.25436090.9470.95798.36520.25
2.795-2.8860.2521790.2332590.23134880.9570.96598.56650.223
2.886-2.9870.321440.22631770.2333690.9410.96898.57520.216
2.987-3.10.2241810.20630220.20732470.9650.97498.64490.195
3.1-3.2260.2551670.19529060.19831140.9580.97798.68340.184
3.226-3.370.2541460.18428270.18730060.9550.9898.90220.171
3.37-3.5340.2291450.17526530.17828300.9650.98298.86930.164
3.534-3.7240.1921310.15525770.15727320.9780.98599.12150.146
3.724-3.950.1791310.14724340.14825880.9780.98899.11130.14
3.95-4.2210.2011170.14222880.14524230.9760.98899.25710.137
4.221-4.5580.181110.13821400.1422680.980.98999.25040.133
4.558-4.9920.193850.14319650.14520620.9780.98899.4180.141
4.992-5.5780.2361020.16617690.1718820.9720.98699.41550.163
5.578-6.4350.232770.20315660.20416490.9730.98199.63610.198
6.435-7.8660.213640.19413250.19513940.9730.97999.64130.194
7.866-11.0630.163520.15610390.15610940.9840.98699.72580.165
11.063-74.5490.24230.2455820.2456050.9790.961000.246
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)
11.20460.19940.15621.26890.09910.64240.05910.0234-0.0975-0.0723-0.0015-0.0295-0.00240.0397-0.05750.08870.02660.05130.01180.01080.05213.9581-14.7941-18.1853
20.8519-0.2591-0.14150.9118-0.24341.5826-0.0411-0.08230.00770.08020.06540.0911-0.0516-0.124-0.02440.11280.00580.070.0307-0.02710.1229-0.473215.34818.4857
Refinement TLS group
IDRefine-IDRefine TLS-IDSelectionAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1ALLBp1 - 722
2X-RAY DIFFRACTION2ALLAp2 - 721

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