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- PDB-9ssb: Human angiotensin 1-converting enzyme N-domain in complex with zo... -

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Basic information

Entry
Database: PDB / ID: 9ssb
TitleHuman angiotensin 1-converting enzyme N-domain in complex with zofenoprilat
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
ACETATE ION / 3,6,9,12,15,18,21-HEPTAOXATRICOSANE-1,23-DIOL / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / Chem-ZED / Angiotensin-converting enzyme
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 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: 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
B: Angiotensin-converting enzyme, soluble form
C: Angiotensin-converting enzyme, soluble form
D: Angiotensin-converting enzyme, soluble form
hetero molecules


Theoretical massNumber of molelcules
Total (without water)302,12468
Polymers289,9734
Non-polymers12,15164
Water16,988943
1
A: Angiotensin-converting enzyme, soluble form
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,86919
Polymers72,4931
Non-polymers3,37518
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Angiotensin-converting enzyme, soluble form
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,43716
Polymers72,4931
Non-polymers2,94415
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Angiotensin-converting enzyme, soluble form
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,76020
Polymers72,4931
Non-polymers3,26619
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Angiotensin-converting enzyme, soluble form
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,05913
Polymers72,4931
Non-polymers2,56512
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)73.532, 101.88, 114.274
Angle α, β, γ (deg.)84.902, 85.457, 81.349
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
32A
42C
53A
63D
74B
84C
95B
105D
116C
126D

NCS domain segments:

Beg auth comp-ID: LEU / Beg label comp-ID: LEU

Dom-IDComponent-IDEns-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111TYRTYRAA1 - 6071 - 607
211TYRTYRBB1 - 6071 - 607
322PROPROAA1 - 6081 - 608
422PROPROCC1 - 6081 - 608
533TYRTYRAA1 - 6071 - 607
633TYRTYRDD1 - 6071 - 607
744TYRTYRBB1 - 6071 - 607
844TYRTYRCC1 - 6071 - 607
955ILEILEBB1 - 6111 - 611
1055ILEILEDD1 - 6111 - 611
1166TYRTYRCC1 - 6071 - 607
1266TYRTYRDD1 - 6071 - 607

NCS ensembles :
IDDetails
1Local NCS retraints between domains: 1 2
2Local NCS retraints between domains: 3 4
3Local NCS retraints between domains: 5 6
4Local NCS retraints between domains: 7 8
5Local NCS retraints between domains: 9 10
6Local NCS retraints between domains: 11 12

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Angiotensin-converting enzyme, soluble form


Mass: 72493.352 Da / Num. of mol.: 4
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 , 6 types, 12 molecules

#2: Polysaccharide alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1- ...alpha-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.: 3
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-4DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1a_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)][a-D-Manp]{}}[(6+1)][a-L-Fucp]{}}LINUCSPDB-CARE
#3: Polysaccharide alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 367.349 Da / Num. of mol.: 3
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
#4: 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
#5: Polysaccharide alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 1 / Source method: obtained synthetically
DescriptorTypeProgram
DManpa1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1a_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][a-D-Manp]{}}}LINUCSPDB-CARE
#6: 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.: 3 / Source method: obtained synthetically
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
#14: 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 , 14 types, 995 molecules

#7: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#8: Chemical
ChemComp-ZED / L-PROLINE, 1-[(2S)-3-MERCAPTO-2-METHYL-1-OXOPROPYL]-4-(PHENYLTHIO)-, 4S / ZOFENOPRILAT


Mass: 325.446 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C15H19NO3S2 / Feature type: SUBJECT OF INVESTIGATION / Comment: inhibitor*YM
#9: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


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


Mass: 62.068 Da / Num. of mol.: 17 / Source method: obtained synthetically / Formula: C2H6O2
#11: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#12: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H14O4
#13: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#15: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: Cl
#16: Chemical ChemComp-12P / DODECAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400


Mass: 546.646 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H50O13 / Comment: precipitant*YM
#17: Chemical ChemComp-PE8 / 3,6,9,12,15,18,21-HEPTAOXATRICOSANE-1,23-DIOL


Mass: 370.436 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H34O9
#18: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#19: Chemical ChemComp-XPE / 3,6,9,12,15,18,21,24,27-NONAOXANONACOSANE-1,29-DIOL / DECAETHYLENE GLYCOL


Mass: 458.541 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H42O11 / Comment: precipitant*YM
#20: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#21: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 943 / 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: 3 Å3/Da / Density % sol: 59.06 %
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→72.53 Å / Num. obs: 216060 / % possible obs: 98.1 % / Redundancy: 3.5 % / CC1/2: 0.988 / Rpim(I) all: 0.08 / Net I/σ(I): 6
Reflection shellResolution: 2→2.03 Å / Num. unique obs: 10632 / CC1/2: 0.417 / Rpim(I) all: 0.765

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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→72.53 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.942 / SU B: 9.817 / SU ML: 0.129 / Cross valid method: THROUGHOUT / ESU R: 0.176 / ESU R Free: 0.15
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflectionSelection details
Rfree0.2257 10581 4.898 %RANDOM
Rwork0.2009 205438 --
all0.202 ---
obs-216019 98.082 %-
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: 30.339 Å2
Baniso -1Baniso -2Baniso -3
1--1.524 Å2-0.509 Å20.542 Å2
2---0.102 Å2-0.729 Å2
3---1.415 Å2
Refinement stepCycle: LAST / Resolution: 2→72.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19793 0 777 943 21513
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.01221503
X-RAY DIFFRACTIONr_bond_other_d0.0010.01619378
X-RAY DIFFRACTIONr_angle_refined_deg1.6051.81829217
X-RAY DIFFRACTIONr_angle_other_deg0.5681.74744737
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.04352470
X-RAY DIFFRACTIONr_dihedral_angle_2_deg9.095142
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.466103257
X-RAY DIFFRACTIONr_dihedral_angle_6_deg14.833101069
X-RAY DIFFRACTIONr_chiral_restr0.0820.23060
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0225385
X-RAY DIFFRACTIONr_gen_planes_other0.0010.025243
X-RAY DIFFRACTIONr_nbd_refined0.2210.24475
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1770.216519
X-RAY DIFFRACTIONr_nbtor_refined0.1860.210496
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0770.210578
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1710.2839
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0180.22
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.170.230
X-RAY DIFFRACTIONr_nbd_other0.1730.2120
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1730.229
X-RAY DIFFRACTIONr_mcbond_it1.5351.8219835
X-RAY DIFFRACTIONr_mcbond_other1.5331.8189824
X-RAY DIFFRACTIONr_mcangle_it2.3843.25912310
X-RAY DIFFRACTIONr_mcangle_other2.3843.2612311
X-RAY DIFFRACTIONr_scbond_it2.6752.28611668
X-RAY DIFFRACTIONr_scbond_other2.6752.28611669
X-RAY DIFFRACTIONr_scangle_it4.2594.03216907
X-RAY DIFFRACTIONr_scangle_other4.2594.03216908
X-RAY DIFFRACTIONr_lrange_it5.40319.68724377
X-RAY DIFFRACTIONr_lrange_other5.40319.68824378
X-RAY DIFFRACTIONr_ncsr_local_group_10.0680.0521285
X-RAY DIFFRACTIONr_ncsr_local_group_20.0570.0521390
X-RAY DIFFRACTIONr_ncsr_local_group_30.0580.0521387
X-RAY DIFFRACTIONr_ncsr_local_group_40.0690.0521412
X-RAY DIFFRACTIONr_ncsr_local_group_50.0590.0521767
X-RAY DIFFRACTIONr_ncsr_local_group_60.0620.0521544
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AX-RAY DIFFRACTIONLocal ncs0.06770.05009
12BX-RAY DIFFRACTIONLocal ncs0.06770.05009
23AX-RAY DIFFRACTIONLocal ncs0.056650.05009
24CX-RAY DIFFRACTIONLocal ncs0.056650.05009
35AX-RAY DIFFRACTIONLocal ncs0.058120.05009
36DX-RAY DIFFRACTIONLocal ncs0.058120.05009
47BX-RAY DIFFRACTIONLocal ncs0.068810.05009
48CX-RAY DIFFRACTIONLocal ncs0.068810.05009
59BX-RAY DIFFRACTIONLocal ncs0.058970.05009
510DX-RAY DIFFRACTIONLocal ncs0.058970.05009
611CX-RAY DIFFRACTIONLocal ncs0.062450.05009
612DX-RAY DIFFRACTIONLocal ncs0.062450.05009
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)
10.68070.175-0.12960.7588-0.25880.99370.01050.04780.04130.052-0.01430.0058-0.0347-0.00350.00390.0417-0.0098-0.01130.014-0.01470.0609-15.4108-76.4596-2.0942
21.1255-0.15430.07420.6870.20610.58420.03370.0748-0.08440.0098-0.0085-0.00940.03980.0266-0.02530.0464-0.0207-0.01750.01970.00160.0117-2.5683-23.73930.8849
30.53990.13560.06750.8911-0.28151.0620.00430.03330.03820.04770.0038-0.0542-0.07440.0818-0.00810.0433-0.0064-0.01020.0116-0.01640.093931.8081-18.005855.7347
41.2106-0.20050.06010.70270.2680.55710.01550.0843-0.03680.0166-0.0032-0.00280.02320.0043-0.01230.0228-0.0163-0.01450.02030.00840.009928.5149-66.244258.9963
Refinement TLS group
IDRefine-IDRefine TLS-IDSelectionAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1ALLAp1 - 736
2X-RAY DIFFRACTION2ALLBp1 - 739
3X-RAY DIFFRACTION3ALLCp1 - 740
4X-RAY DIFFRACTION4ALLDp1 - 734

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