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- PDB-7z70: Crystal structure of Angiotensin-1 converting enzyme C-domain in ... -

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Basic information

Entry
Database: PDB / ID: 7z70
TitleCrystal structure of Angiotensin-1 converting enzyme C-domain in complex with fosinoprilat
ComponentsAngiotensin-converting enzyme
KeywordsHYDROLASE / Angiotensin-1 converting enzyme / fosinoprilat / fosinopril / Metalloprotease
Function / homology
Function and homology information


mononuclear cell proliferation / cell proliferation in bone marrow / bradykinin receptor binding / regulation of angiotensin metabolic process / exopeptidase activity / substance P catabolic process / peptidyl-dipeptidase A / tripeptidyl-peptidase activity / regulation of renal output by angiotensin / negative regulation of calcium ion import ...mononuclear cell proliferation / cell proliferation in bone marrow / bradykinin receptor binding / regulation of angiotensin metabolic process / exopeptidase activity / substance P catabolic process / peptidyl-dipeptidase A / tripeptidyl-peptidase activity / regulation of renal output by angiotensin / negative regulation of calcium ion import / positive regulation of peptidyl-cysteine S-nitrosylation / response to laminar fluid shear stress / negative regulation of gap junction assembly / metallodipeptidase activity / positive regulation of systemic arterial blood pressure / cellular response to aldosterone / hormone catabolic process / bradykinin catabolic process / angiogenesis involved in coronary vascular morphogenesis / response to thyroid hormone / antigen processing and presentation of peptide antigen via MHC class I / negative regulation of glucose import / vasoconstriction / hormone metabolic process / neutrophil mediated immunity / regulation of smooth muscle cell migration / regulation of hematopoietic stem cell proliferation / 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 / arachidonic acid secretion / post-transcriptional regulation of gene expression / eating behavior / heterocyclic compound binding / lung alveolus development / heart contraction / peptide catabolic process / response to dexamethasone / regulation of heart rate by cardiac conduction / regulation of systemic arterial blood pressure by renin-angiotensin / regulation of vasoconstriction / peptidyl-dipeptidase activity / hematopoietic stem cell differentiation / blood vessel remodeling / angiotensin maturation / amyloid-beta metabolic process / animal organ regeneration / Metabolism of Angiotensinogen to Angiotensins / carboxypeptidase activity / positive regulation of vasoconstriction / sperm midpiece / blood vessel diameter maintenance / response to nutrient levels / basal plasma membrane / kidney development / angiotensin-activated signaling pathway / female pregnancy / cellular response to glucose stimulus / brush border membrane / regulation of synaptic plasticity / metalloendopeptidase activity / regulation of blood pressure / metallopeptidase activity / male gonad development / peptidase activity / actin binding / spermatogenesis / endopeptidase activity / response to lipopolysaccharide / lysosome / calmodulin binding / response to hypoxia / endosome / response to xenobiotic stimulus / positive regulation of apoptotic process / external side of plasma membrane / negative regulation of gene expression / proteolysis / extracellular space / zinc ion binding / extracellular exosome / extracellular region / plasma membrane
Similarity search - Function
Peptidase family M2 domain profile. / Peptidase M2, peptidyl-dipeptidase A / Angiotensin-converting enzyme / Neutral zinc metallopeptidases, zinc-binding region signature.
Similarity search - Domain/homology
ACETATE ION / BORIC ACID / IMIDAZOLE / fosinoprilat / Angiotensin-converting enzyme
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 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: Febs J. / Year: 2022
Title: Structural basis for the inhibition of human angiotensin-1 converting enzyme by fosinoprilat.
Authors: Cozier, G.E. / Newby, E.C. / Schwager, S.L.U. / Isaac, R.E. / Sturrock, E.D. / Acharya, K.R.
History
DepositionMar 14, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 22, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 16, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Angiotensin-converting enzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,00414
Polymers68,8781
Non-polymers2,12613
Water10,665592
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)56.563, 85.987, 134.686
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

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Protein , 1 types, 1 molecules A

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


Mass: 68877.875 Da / Num. of mol.: 1 / Mutation: E64G, N90Q, N155Q, N337Q, N586Q
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 , 2 types, 2 molecules

#2: Polysaccharide alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-3)-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: 894.823 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3DManpb1-4DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/4,5,4/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5][a1221m-1a_1-5]/1-1-2-3-4/a4-b1_a6-e1_b4-c1_c3-d1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}}}[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
#4: 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, 603 molecules

#3: Chemical ChemComp-KS8 / fosinoprilat


Mass: 435.494 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H34NO5P / Feature type: SUBJECT OF INVESTIGATION / Comment: inhibitor*YM
#5: Chemical ChemComp-BO3 / BORIC ACID


Mass: 61.833 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: BH3O3
#6: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#7: Chemical ChemComp-IMD / IMIDAZOLE


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


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#9: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#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.: 592 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.38 Å3/Da / Density % sol: 48.27 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 4 / Details: 0.1 M MIB 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: 0.9795 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Feb 5, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.85→134.69 Å / Num. obs: 56970 / % possible obs: 100 % / Redundancy: 13 % / Biso Wilson estimate: 21.83 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.341 / Rpim(I) all: 0.098 / Net I/σ(I): 5.2
Reflection shellResolution: 1.85→1.89 Å / Mean I/σ(I) obs: 0.7 / Num. unique obs: 3456 / CC1/2: 0.327

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Processing

Software
NameVersionClassification
PHENIX1.19.1_4122refinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6F9T

6f9t


Resolution: 1.85→52.15 Å / SU ML: 0.2418 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.3981
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2134 2017 3.57 %
Rwork0.1736 54491 -
obs0.175 56508 99.32 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 26.35 Å2
Refinement stepCycle: LAST / Resolution: 1.85→52.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4690 0 136 592 5418
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00545009
X-RAY DIFFRACTIONf_angle_d0.76806
X-RAY DIFFRACTIONf_chiral_restr0.043728
X-RAY DIFFRACTIONf_plane_restr0.0063871
X-RAY DIFFRACTIONf_dihedral_angle_d14.90281856
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.85-1.90.36031450.31593813X-RAY DIFFRACTION98.78
1.9-1.950.28771640.27723822X-RAY DIFFRACTION98.91
1.95-20.31881400.263793X-RAY DIFFRACTION98.97
2-2.070.26011260.22333852X-RAY DIFFRACTION99
2.07-2.140.23891230.2073861X-RAY DIFFRACTION99.03
2.14-2.230.26041460.18913823X-RAY DIFFRACTION99.15
2.23-2.330.21891420.18213882X-RAY DIFFRACTION99.09
2.33-2.450.20981520.16153869X-RAY DIFFRACTION99.28
2.45-2.610.2021470.15813852X-RAY DIFFRACTION99.58
2.61-2.810.20741390.15993905X-RAY DIFFRACTION99.63
2.81-3.090.21451450.15713924X-RAY DIFFRACTION99.78
3.09-3.540.19831420.15223954X-RAY DIFFRACTION99.71
3.54-4.460.17741430.14023994X-RAY DIFFRACTION99.9
4.46-52.150.17561630.16254147X-RAY DIFFRACTION99.68
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)
11.32563985595-0.864063989548-0.5636285166016.419475017323.328330579253.030672833970.0486762500060.143824471704-0.1154730886450.000252168457645-0.2706669260180.05769977122210.239198849427-0.1483695093420.1801942733990.215152592102-0.02684873657920.005669267870980.288083908115-0.01198107685090.15810541070411.0849885895-6.898617569261.17408775117
22.232744513561.51242740045-0.139749902281.772915914460.7612050601051.67991656352-0.1696010316950.136232501863-0.103430845581-0.3267042150170.01937076407870.3449109728530.204280915521-0.02683260854930.1276405982950.235699328143-0.0048001878794-0.006366563452650.257695205795-0.001118434800090.1248999351763.63465797901-7.594573557294.63594092672
30.6080211412650.3010784854590.1735972138212.140429629450.59788143090.948019659498-0.006599107069090.04773644645370.11152038479-0.232045873539-0.01736353664480.0719290087302-0.17045880253-0.06140810276250.04637854399010.142895836920.006169576711750.004440725422980.1756617782240.01869562836370.1518700456280.67220712155412.078742889320.6695368483
40.541982848184-0.6945410891190.3297728604683.656984125922.469508591383.400374271370.0291286537127-0.0261514665005-0.03165227781980.594980231639-0.0206627381399-0.112945891380.346188860056-0.0175334182047-0.005414411190870.124465664901-0.0007799564277280.01049833055720.1790485405520.007217110055970.13998468357810.03317577365.5580399480842.9700359727
51.00434575932-0.313874558350.05582076997461.226375636470.5020316309841.952142745672.53483129256E-5-0.002107983042260.1021737512270.00554073483380.119457808698-0.170455738925-0.2011180948480.223644918601-0.08702635269640.17176366065-0.0116650528274-0.007933945903080.164983644013-0.0210587421860.17527344303613.963628151918.584701394440.8433441016
61.75107990767-0.2634352430250.3966694745082.175271480420.2905037309981.73232254839-0.02817233926660.1022659565780.141689177669-0.1470505534780.0538001948938-0.172832223737-0.141256313610.211995873299-0.01960656775040.155675392166-0.04332055648170.0328950851740.1790249071210.009770358209360.16032430135623.912750156410.723898592315.2217094742
71.15778277271-0.193666162379-0.294437548121.41927195268-0.08419543726331.08201699411-0.054180787241-0.07224509607060.1553182952550.02913271410490.0767204810835-0.245561761136-0.07329666122510.205702349477-0.0274123508710.07416776908680.013188739904-0.00413461039940.16394688113-0.01171287336830.18832156754725.10097695444.6565586805328.7405098286
8-0.00140059400729-0.00410806824050.03991333035131.037020007880.1521134393340.822877222704-0.01908141431590.03770329355260.03590633717090.028391255407-0.02000725362040.08252687212270.0039241244427-0.08311926021320.04377805295160.126071853624-0.0121974647202-0.004761723131560.1584956874050.001676455694610.1479804333573.733213166095.0275209695630.2699422001
92.502900388120.587335201702-0.05496218361730.6863720292060.4515054384450.827790341595-0.130472139322-0.119950823943-0.11933749890.1100404082270.136900788699-0.1673909747550.1756130014620.346574524925-0.04356539464450.1473456288470.0528040915667-0.01352993160130.247864838256-0.03612159963020.2596758402332.3896166339-4.1943176018327.9220653802
100.614369142216-0.558406540296-0.3899298521262.157372171372.075164963.65387695969-0.0735404947321-0.0591895650066-0.01259218597820.3019579068480.179036067865-0.19306280940.2165310479510.259567418381-0.08256711508580.158111399643-0.00471241232942-0.02507516852220.1413093494110.02970819985820.15485303962417.6842897975-2.5751190288439.7997072336
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid 40 through 70 )40 - 701 - 31
22chain 'A' and (resid 71 through 128 )71 - 12832 - 89
33chain 'A' and (resid 129 through 228 )129 - 22890 - 189
44chain 'A' and (resid 229 through 259 )229 - 259190 - 220
55chain 'A' and (resid 260 through 300 )260 - 300221 - 261
66chain 'A' and (resid 301 through 393 )301 - 393262 - 354
77chain 'A' and (resid 394 through 455 )394 - 455355 - 413
88chain 'A' and (resid 456 through 540 )456 - 540414 - 498
99chain 'A' and (resid 541 through 568 )541 - 568499 - 526
1010chain 'A' and (resid 569 through 617 )569 - 617527 - 575

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