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

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Basic information

Entry
Database: PDB / ID: 9gbs
TitleHuman Angiotensin-1 converting enzyme N-domain in complex with a diprolyl inhibitor- SG18
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 / 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
: / alpha-L-fucopyranose / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / 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)151,02837
Polymers144,9872
Non-polymers6,04235
Water11,872659
1
A: Angiotensin-converting enzyme, soluble form
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,48318
Polymers72,4931
Non-polymers2,99017
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Angiotensin-converting enzyme, soluble form
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,54519
Polymers72,4931
Non-polymers3,05218
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)72.723, 77.164, 81.841
Angle α, β, γ (deg.)88.371, 64.577, 75.247
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 , 3 types, 11 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
#8: 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.: 9 / 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
#13: Sugar ChemComp-FUC / alpha-L-fucopyranose / alpha-L-fucose / 6-deoxy-alpha-L-galactopyranose / L-fucose / fucose


Type: L-saccharide, alpha linking / Mass: 164.156 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H12O5
IdentifierTypeProgram
LFucpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-L-fucopyranoseCOMMON NAMEGMML 1.0
a-L-FucpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
FucSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 10 types, 683 molecules

#3: Chemical ChemComp-A1IJY / (2S)-1-[(2S)-2-[[(1S)-1-[(2S)-1-(4-carboxyphenyl)carbonylpyrrolidin-2-yl]-2-oxidanyl-2-oxidanylidene-ethyl]amino]propanoyl]pyrrolidine-2-carboxylic acid


Mass: 461.465 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C22H27N3O8
#4: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


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


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical
ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H14O4
#7: Chemical ChemComp-P6G / HEXAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400


Mass: 282.331 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H26O7 / Comment: precipitant*YM
#9: Chemical ChemComp-ZN / ZINC ION


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


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#11: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#12: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


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


Mass: 18.015 Da / Num. of mol.: 659 / 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: 2.86 Å3/Da / Density % sol: 57.05 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, hanging drop
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: I03 / Wavelength: 0.9763 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Aug 4, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.9→73.6 Å / Num. obs: 119232 / % possible obs: 97.8 % / Redundancy: 7.1 % / CC1/2: 0.996 / Rpim(I) all: 0.063 / Net I/σ(I): 7.5
Reflection shellResolution: 1.9→1.93 Å / Num. unique obs: 5836 / CC1/2: 0.433 / Rpim(I) all: 1.629

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→63.722 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.961 / SU B: 3.816 / SU ML: 0.105 / Cross valid method: FREE R-VALUE / ESU R: 0.129 / ESU R Free: 0.124 / Details: Hydrogens have not been used
RfactorNum. reflection% reflection
Rfree0.2041 5877 4.93 %
Rwork0.165 113340 -
all0.167 --
obs-119217 97.757 %
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: 36.005 Å2
Baniso -1Baniso -2Baniso -3
1--0.098 Å21.169 Å21.014 Å2
2--0.863 Å21.258 Å2
3---0.11 Å2
Refinement stepCycle: LAST / Resolution: 1.9→63.722 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9860 0 389 659 10908
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.01210731
X-RAY DIFFRACTIONr_angle_refined_deg2.41.83114583
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.56751241
X-RAY DIFFRACTIONr_dihedral_angle_2_deg8.764570
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.482101632
X-RAY DIFFRACTIONr_dihedral_angle_6_deg15.43510535
X-RAY DIFFRACTIONr_chiral_restr0.1550.21507
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.028509
X-RAY DIFFRACTIONr_nbd_refined0.2370.25233
X-RAY DIFFRACTIONr_nbtor_refined0.3230.27344
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1540.2691
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.20.257
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1530.212
X-RAY DIFFRACTIONr_mcbond_it4.0833.1754917
X-RAY DIFFRACTIONr_mcangle_it5.1135.6846172
X-RAY DIFFRACTIONr_scbond_it6.6043.7665814
X-RAY DIFFRACTIONr_scangle_it9.0646.6048410
X-RAY DIFFRACTIONr_lrange_it9.97737.02716938
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
1.9-1.9490.3034210.28882930.28990400.9270.93296.39380.294
1.949-2.0030.2874180.26780380.26887530.9390.94296.60690.271
2.003-2.0610.2824120.24778530.24985310.9360.95296.8820.249
2.061-2.1240.2533930.22576590.22783120.9540.96196.8720.223
2.124-2.1940.2433850.274440.20280500.960.97297.25470.196
2.194-2.2710.2373840.18472130.18678160.9630.97697.19810.178
2.271-2.3560.233420.17669770.17874980.9630.9897.61270.171
2.356-2.4520.2343260.17667130.17972030.9660.9897.72320.17
2.452-2.5610.2543580.16764500.17169510.9630.98397.94270.161
2.561-2.6860.2273110.15961930.16266260.970.98598.15880.155
2.686-2.8310.2063000.16258820.16463030.9730.98598.08030.159
2.831-3.0020.2132930.15855590.16159510.970.98598.33640.158
3.002-3.2090.2122920.16252220.16556120.9740.98498.25370.165
3.209-3.4650.2122430.16249140.16552200.9740.98598.79310.168
3.465-3.7950.172380.14445000.14547880.9820.98998.95570.153
3.795-4.2410.1682240.12240790.12543370.9840.99199.2160.137
4.241-4.8930.1611870.13136110.13338230.9830.9999.34610.15
4.893-5.9840.1711610.14430660.14532450.9850.98999.44530.165
5.984-8.4260.1551150.16323670.16325000.9860.98799.280.185
8.426-63.7220.176740.17213050.17313920.9820.98399.06610.257

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