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- PDB-9gbq: Human Angiotensin-1 converting enzyme N-domain in complex with a ... -

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Basic information

Entry
Database: PDB / ID: 9gbq
TitleHuman Angiotensin-1 converting enzyme N-domain in complex with a diprolyl inhibitor- SG15
ComponentsAngiotensin-converting enzyme, soluble form
KeywordsHYDROLASE / Inhibitor / complex / protease
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 / regulation of heart rate by cardiac conduction / antigen processing and presentation of peptide antigen via MHC class I / 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
: / DI(HYDROXYETHYL)ETHER / Angiotensin-converting enzyme
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsGregory, K.S. / Cozier, G.E. / 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 human angiotensin-1 converting enzyme inhibition by a series of diprolyl-derived compounds.
Authors: Gregory, K.S. / Cozier, G.E. / Fienberg, S. / Chibale, K. / Sturrock, E.D. / Acharya, K.R.
History
DepositionJul 31, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 22, 2025Provider: repository / Type: Initial release
Revision 1.1Mar 19, 2025Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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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)149,42921
Polymers144,9872
Non-polymers4,44219
Water10,160564
1
A: Angiotensin-converting enzyme, soluble form
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,87511
Polymers72,4931
Non-polymers2,38110
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Angiotensin-converting enzyme, soluble form
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,55410
Polymers72,4931
Non-polymers2,0619
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)72.493, 77.175, 81.441
Angle α, β, γ (deg.)88.549, 64.518, 75.143
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: 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 , 4 types, 6 molecules

#2: Polysaccharide alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 367.349 Da / Num. of mol.: 1
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
#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 beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-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: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}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.: 3 / 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, 577 molecules

#6: Chemical ChemComp-P33 / 3,6,9,12,15,18-HEXAOXAICOSANE-1,20-DIOL / HEPTAETHYLENE GLYCOL / PEG330


Mass: 326.383 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H30O8 / Comment: precipitant*YM
#7: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H10O3
#8: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#9: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#10: Chemical ChemComp-A1IJZ / (2S)-1-[(2S)-2-[[(1S)-1-[(2S)-1-[(2S)-2-azanyl-3-phenyl-propanoyl]pyrrolidin-2-yl]-2-oxidanyl-2-oxidanylidene-ethyl]amino]propanoyl]pyrrolidine-2-carboxylic acid


Mass: 460.523 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C23H32N4O6 / Feature type: SUBJECT OF INVESTIGATION
#11: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#12: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#13: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 564 / 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: 2.84 Å3/Da / Density % sol: 56.69 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 1 M Tris/Bicine pH8.5 60 mM divalent cations (MgCl2 and CaCl2) 30% PEG550 MME/PEG20K

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Sep 8, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.9→74.24 Å / Num. obs: 118206 / % possible obs: 97.8 % / Redundancy: 6.8 % / CC1/2: 0.997 / Rpim(I) all: 0.052 / Net I/σ(I): 8.6
Reflection shellResolution: 1.9→1.93 Å / Num. unique obs: 5766 / CC1/2: 0.533 / Rpim(I) all: 1.174

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→73.276 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.956 / WRfactor Rfree: 0.22 / WRfactor Rwork: 0.182 / SU B: 8.846 / SU ML: 0.111 / Average fsc free: 0.9617 / Average fsc work: 0.9717 / Cross valid method: FREE R-VALUE / ESU R: 0.135 / ESU R Free: 0.127 / Details: Hydrogens have not been used
RfactorNum. reflection% reflection
Rfree0.2119 5892 4.986 %
Rwork0.1773 112280 -
all0.179 --
obs-118172 97.815 %
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: 37.895 Å2
Baniso -1Baniso -2Baniso -3
1--0.435 Å20.886 Å21.36 Å2
2--0.529 Å20.862 Å2
3---0.84 Å2
Refinement stepCycle: LAST / Resolution: 1.9→73.276 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9851 0 288 564 10703
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.01210470
X-RAY DIFFRACTIONr_angle_refined_deg2.2891.83214253
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.91351201
X-RAY DIFFRACTIONr_dihedral_angle_2_deg8.532565
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.505101595
X-RAY DIFFRACTIONr_dihedral_angle_6_deg14.73610527
X-RAY DIFFRACTIONr_chiral_restr0.160.21493
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.028318
X-RAY DIFFRACTIONr_nbd_refined0.2240.25205
X-RAY DIFFRACTIONr_nbtor_refined0.3220.27180
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1630.2639
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2480.249
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1350.27
X-RAY DIFFRACTIONr_mcbond_it2.4152.0664819
X-RAY DIFFRACTIONr_mcangle_it3.4293.6986015
X-RAY DIFFRACTIONr_scbond_it4.1232.5415651
X-RAY DIFFRACTIONr_scangle_it6.0784.4628238
X-RAY DIFFRACTIONr_lrange_it7.2123.716611
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
1.9-1.9490.3154340.28682000.28789450.9260.93796.52320.29
1.949-2.0030.2964400.26379520.26586770.9410.94896.71550.265
2.003-2.0610.2734350.23977910.24184950.9420.95696.83340.236
2.061-2.1240.2464200.22775750.22882460.9610.96296.95610.222
2.124-2.1940.2423600.21173540.21279410.9570.96997.14140.204
2.194-2.2710.2373850.19971590.20177370.9630.97397.50550.192
2.271-2.3560.2423690.19368750.19674330.9620.97697.45730.186
2.356-2.4520.2383810.19165850.19471270.9660.97697.7410.184
2.452-2.5610.2413090.17964240.18268680.9640.9898.03440.173
2.561-2.6860.2253410.17961150.18265800.9670.98198.11550.174
2.686-2.8310.2042830.17758690.17862590.9730.98198.29050.173
2.831-3.0030.232760.18255140.18458850.9680.9898.38570.181
3.003-3.210.2282560.1852040.18255360.9680.98198.62720.182
3.21-3.4660.2032340.17448790.17551800.9760.98398.70660.179
3.466-3.7960.1972140.15944860.16147500.9790.98798.94740.168
3.796-4.2430.1632160.13540530.13643050.9840.9999.16380.147
4.243-4.8960.1591960.1335660.13237870.9860.9999.33990.145
4.896-5.990.1841550.15630320.15732040.9810.98799.46940.173
5.99-8.4430.2131250.18223460.18324820.9830.98599.55680.199
8.443-73.2760.182630.18713010.18613740.9810.98199.27220.252
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)
11.1115-0.13210.10261.32870.27580.54010.11410.0792-0.075-0.0856-0.04230.042-0.0166-0.011-0.07170.03220.042-0.00010.06880.01060.02062.676-16.1472-17.5764
20.8952-0.3292-0.2951.27370.4282.0752-0.0243-0.1165-0.03580.09870.01620.02550.0636-0.060.0080.03490.00870.02980.037-0.00180.0493-0.760913.747419.1039
Refinement TLS groupSelection: ALL

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