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- PDB-7q26: Crystal structure of Angiotensin-1 converting enzyme N-domain in ... -

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Basic information

Entry
Database: PDB / ID: 7q26
TitleCrystal structure of Angiotensin-1 converting enzyme N-domain in complex with dual ACE/NEP inhibitor AD013
ComponentsAngiotensin-converting enzyme
KeywordsHYDROLASE / Angiotensin-1 converting enzyme / Dual inhibitor / NEP / 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 / positive regulation of peptidyl-cysteine S-nitrosylation ...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 / positive regulation of peptidyl-cysteine S-nitrosylation / negative regulation of calcium ion import / response to laminar fluid shear stress / negative regulation of gap junction assembly / metallodipeptidase activity / hormone catabolic process / bradykinin catabolic process / cellular response to aldosterone / angiogenesis involved in coronary vascular morphogenesis / response to thyroid hormone / negative regulation of D-glucose import / vasoconstriction / regulation of smooth muscle cell migration / neutrophil mediated immunity / regulation of hematopoietic stem cell proliferation / hormone metabolic process / mitogen-activated protein kinase binding / embryo development ending in birth or egg hatching / chloride ion binding / mitogen-activated protein kinase kinase binding / positive regulation of neurogenesis / arachidonate secretion / post-transcriptional regulation of gene expression / eating behavior / heterocyclic compound binding / peptide catabolic process / lung alveolus development / heart contraction / antigen processing and presentation of peptide antigen via MHC class I / positive regulation of systemic arterial blood pressure / response to dexamethasone / 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 / animal organ regeneration / peptidyl-dipeptidase activity / Metabolism of Angiotensinogen to Angiotensins / angiotensin maturation / metallocarboxypeptidase activity / positive regulation of vasoconstriction / sperm midpiece / blood vessel diameter maintenance / basal plasma membrane / kidney development / angiotensin-activated signaling pathway / female pregnancy / brush border membrane / response to nutrient levels / cellular response to glucose stimulus / regulation of synaptic plasticity / metalloendopeptidase activity / regulation of blood pressure / male gonad development / metallopeptidase activity / peptidase activity / actin binding / spermatogenesis / endopeptidase activity / response to lipopolysaccharide / response to hypoxia / lysosome / calmodulin binding / endosome / positive regulation of apoptotic process / response to xenobiotic stimulus / external side of plasma membrane / negative regulation of gene expression / 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-8JV / ACETATE ION / 3,6,9,12,15,18,21-HEPTAOXATRICOSANE-1,23-DIOL / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / Angiotensin-converting enzyme
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsCozier, G.E. / Acharya, K.R.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom)MR/M026647/1 United Kingdom
CitationJournal: J.Med.Chem. / Year: 2022
Title: Probing the Requirements for Dual Angiotensin-Converting Enzyme C-Domain Selective/Neprilysin Inhibition.
Authors: Arendse, L.B. / Cozier, G.E. / Eyermann, C.J. / Basarab, G.S. / Schwager, S.L. / Chibale, K. / Acharya, K.R. / Sturrock, E.D.
History
DepositionOct 23, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 16, 2022Provider: repository / Type: Initial release
Revision 1.1Mar 9, 2022Group: 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
Revision 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Angiotensin-converting enzyme
B: Angiotensin-converting enzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)150,86328
Polymers145,2132
Non-polymers5,65026
Water13,637757
1
A: Angiotensin-converting enzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,26714
Polymers72,6071
Non-polymers2,66113
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Angiotensin-converting enzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,59614
Polymers72,6071
Non-polymers2,98913
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)72.888, 77.100, 82.621
Angle α, β, γ (deg.)88.634, 64.177, 74.787
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Angiotensin-converting enzyme / ACE / Dipeptidyl carboxypeptidase I / Kininase II


Mass: 72606.508 Da / Num. of mol.: 2
Mutation: N9Q, N25Q, N82Q, N117Q, N131Q, N289Q, Q545R, P576L
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, Hydrolases; Glycosylases; Glycosidases, i.e. enzymes that hydrolyse O- and S-glycosyl compounds, peptidyl-dipeptidase A

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Sugars , 4 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.: 1
Source method: isolated from a genetically manipulated source
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
#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.: 2
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 alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 367.349 Da / Num. of mol.: 2
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
#13: 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 , 12 types, 777 molecules

#5: Chemical ChemComp-8JV / (2~{S},5~{R})-5-(4-methylphenyl)-1-[2-[[(2~{S})-1-oxidanyl-1-oxidanylidene-4-phenyl-butan-2-yl]amino]ethanoyl]pyrrolidine-2-carboxylic acid


Mass: 424.490 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C24H28N2O5 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#7: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#8: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#9: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#10: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#11: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


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


Mass: 62.068 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C2H6O2
#14: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#15: 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
#16: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


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


Mass: 18.015 Da / Num. of mol.: 757 / 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: 2.76 Å3/Da / Density % sol: 55.47 %
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: I04-1 / Wavelength: 0.9159 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Dec 4, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9159 Å / Relative weight: 1
ReflectionResolution: 1.7→73.97 Å / Num. obs: 165914 / % possible obs: 97 % / Redundancy: 6.9 % / Biso Wilson estimate: 24.81 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.068 / Rpim(I) all: 0.032 / Net I/σ(I): 13.3
Reflection shellResolution: 1.7→1.73 Å / Redundancy: 6.6 % / Mean I/σ(I) obs: 1.9 / Num. unique obs: 8167 / CC1/2: 0.72 / % possible all: 95.8

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Processing

Software
NameVersionClassification
PHENIX1.19.1_4122refinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6F9V

6f9v


Resolution: 1.7→55.27 Å / SU ML: 0.2233 / Cross valid method: FREE R-VALUE / σ(F): 2.01 / Phase error: 24.1547
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2154 1947 1.17 %
Rwork0.195 163897 -
obs0.1952 165844 96.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 39.02 Å2
Refinement stepCycle: LAST / Resolution: 1.7→55.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9879 0 370 757 11006
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00310700
X-RAY DIFFRACTIONf_angle_d0.648414553
X-RAY DIFFRACTIONf_chiral_restr0.03891526
X-RAY DIFFRACTIONf_plane_restr0.00481874
X-RAY DIFFRACTIONf_dihedral_angle_d14.11153932
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.740.34431550.325611528X-RAY DIFFRACTION95.83
1.74-1.790.31461370.290211634X-RAY DIFFRACTION95.96
1.79-1.840.27181320.268711593X-RAY DIFFRACTION95.99
1.84-1.90.26071400.251911584X-RAY DIFFRACTION96.33
1.9-1.970.23151460.239211661X-RAY DIFFRACTION96.16
1.97-2.050.24481250.235911596X-RAY DIFFRACTION96.56
2.05-2.140.23211170.225611760X-RAY DIFFRACTION96.65
2.14-2.250.25211420.212511650X-RAY DIFFRACTION97.01
2.25-2.40.2481760.205411746X-RAY DIFFRACTION97.28
2.4-2.580.22631090.202111801X-RAY DIFFRACTION97.44
2.58-2.840.21471370.202611810X-RAY DIFFRACTION97.91
2.84-3.250.23551550.191711787X-RAY DIFFRACTION98.05
3.25-4.10.17561440.163711878X-RAY DIFFRACTION98.26
4.1-55.270.17191320.158911869X-RAY DIFFRACTION98.28
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)
12.187744828470.6128444037250.08828235979980.5498013718440.3413828673960.6719171440080.1867986607920.0389021068623-1.17918738252-0.101735943323-0.3105229262390.1704385407950.171252182545-0.1576760556660.09357392035620.2729512516960.0414106922227-0.1431307536060.412583818109-0.0932039060510.817731975912-76.165321893552.8749752521-18.8902925001
22.94625641106-0.367594291173-0.03185418364871.69369824713-0.1046843679420.1018820100930.216560454141-0.166264948299-0.4806010317150.138585564684-0.1050985675580.2897868678590.0259777271224-0.121228206844-0.1322199132490.291980191056-0.020174545279-0.1598691038420.299542303265-0.008900024016450.517558369334-74.86109250958.9575339648-13.3776170742
32.50231544128-0.116988324168-0.1148420399721.157894121430.06205011859641.408151318420.1298506403640.466714232806-0.00257367340245-0.322655477786-0.117976667038-0.05994932072860.004434562414640.328490088476-0.05141291693310.2956560343820.06605003759640.01628078024620.3643290450640.0663905372580.197674528908-54.874948170676.1102357914-25.2148327502
43.09643000234-0.4057722843660.2913454245091.15236614718-0.007275091065150.5724851403410.0516222310376-0.04141573870250.0401066870526-0.035956050299-0.01277285643880.0118332143385-0.03162774738550.0409789086356-0.03654632554340.180915313921-0.01613439598990.01234392173350.152527695345-0.006402572943090.118494561999-50.069704609472.5432027318-8.5186091446
50.831595266939-0.0952930692227-0.1368788192271.689018726240.3178714745090.4804589975290.2070321305620.2448168710240.0123214890072-0.300596339754-0.21207452309-0.15996503184-0.0544960617921-0.01390199368940.005656441292240.2530309443650.08605795689720.0454495511730.333059355940.03255784645670.195320746766-40.529467297862.5625940041-24.4413557342
61.55609575878-0.2503847937790.131513565951.891632957320.2421654397331.481638752670.1057140901140.151922020633-0.100687892697-0.184047248214-0.1830113098150.0230977964508-0.025481722949-0.1899714921690.06075979537250.1982425658840.0634752753258-0.01122912256650.264946474934-0.04445669592990.1659717148-47.540964266952.6765980739-20.9688875315
72.00457971079-0.8095995875660.1072164060871.488398721180.1287749473680.306809686570.06816680321370.08684459842280.103200008068-0.0241993496124-0.0671866447269-0.0618965933814-0.0616146550520.08243586658730.001261011929250.211547721682-0.01370780300340.01451207102650.2159045936430.03617285605490.176492610866-47.011024746673.6235897383-9.66592724956
81.273719831390.198956021087-0.06820144801362.135571358510.5644007854690.8268210705340.06889463669460.0209963517532-0.09335866448170.0461297065778-0.017602014732-0.1667416668720.05773531822370.0378836442316-0.07155079726360.1953141396320.0154834954595-0.008018376368450.2911126810150.02824790815670.198524209652-39.809427159258.147718651-7.98721785286
90.380676806129-0.310827878649-0.5619787505841.64243931254-0.5051146564451.36116158117-0.265093461869-0.205897861342-0.1774746412620.8035277578050.2995182908480.1685781957560.7149952062660.0730744628803-0.01795739181091.088429597290.2491435390940.05791872566810.5634811875710.05529634171540.400339264669-50.480828800874.111195058840.026934882
101.31801781017-0.828691424205-0.8010152609012.231919555062.102139654212.97398912514-0.0842601606062-0.1101093330460.0156330108130.1470898274110.02065258935830.1296698529950.0112379127301-0.0536041952867-0.002838943650560.203954724849-0.015630611580.01279028578790.1389638867530.0400762672410.211156467101-54.233840301896.374391757218.5780848623
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 1 through 43 )AA1 - 431 - 43
22chain 'A' and (resid 44 through 104 )AA44 - 10444 - 104
33chain 'A' and (resid 105 through 152 )AA105 - 152105 - 147
44chain 'A' and (resid 153 through 237 )AA153 - 237148 - 232
55chain 'A' and (resid 238 through 336 )AA238 - 336233 - 331
66chain 'A' and (resid 337 through 417 )AA337 - 417332 - 412
77chain 'A' and (resid 418 through 498 )AA418 - 498413 - 493
88chain 'A' and (resid 499 through 611 )AA499 - 611494 - 606
99chain 'B' and (resid 2 through 104 )BK2 - 1041 - 103
1010chain 'B' and (resid 105 through 610 )BK105 - 610104 - 603

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