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- PDB-9gbm: Human Angiotensin-1 converting enzyme C-domain in complex with a ... -

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Basic information

Entry
Database: PDB / ID: 9gbm
TitleHuman Angiotensin-1 converting enzyme C-domain in complex with a diprolyl inhibitor- SG3
ComponentsAngiotensin-converting enzyme
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 / antigen processing and presentation of peptide antigen via MHC class I / 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 / regulation of vasoconstriction / peptidyl-dipeptidase activity / 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
: / BORIC ACID / 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,61510
Polymers68,8621
Non-polymers1,7539
Water5,783321
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2250 Å2
ΔGint0 kcal/mol
Surface area22970 Å2
Unit cell
Length a, b, c (Å)55.886, 84.131, 132.664
Angle α, β, γ (deg.)90, 90, 90
Int Tables number19
Space group name H-MP212121

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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: 68861.875 Da / Num. of mol.: 1
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 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
#9: 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 , 7 types, 328 molecules

#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


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


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-BO3 / BORIC ACID


Mass: 61.833 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: BH3O3
#7: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#8: Chemical ChemComp-A1IJW / (2S)-1-[(2S)-2-[[(1S)-1-[(2S)-1-(4-aminophenyl)carbonylpyrrolidin-2-yl]-2-oxidanyl-2-oxidanylidene-ethyl]amino]propanoyl]pyrrolidine-2-carboxylic acid


Mass: 432.470 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H28N4O6 / Feature type: SUBJECT OF INVESTIGATION
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 321 / 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: 2.34 Å3/Da / Density % sol: 47.44 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion / Details: 0.1 M MIB pH 4.0, 5% glycerol, and 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: 0.9159 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Sep 21, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9159 Å / Relative weight: 1
ReflectionResolution: 1.9→132.66 Å / Num. obs: 50194 / % possible obs: 100 % / Redundancy: 12.2 % / CC1/2: 0.996 / Rpim(I) all: 0.057 / Net I/σ(I): 8.5
Reflection shellResolution: 1.9→1.94 Å / Mean I/σ(I) obs: 1.5 / Num. unique obs: 3201 / CC1/2: 0.579 / Rpim(I) all: 0.503

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→71.149 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.945 / WRfactor Rfree: 0.205 / WRfactor Rwork: 0.158 / SU B: 3.808 / SU ML: 0.107 / Average fsc free: 0.961 / Average fsc work: 0.976 / Cross valid method: FREE R-VALUE / ESU R: 0.141 / ESU R Free: 0.138 / Details: Hydrogens have not been used
RfactorNum. reflection% reflection
Rfree0.217 2395 4.78 %
Rwork0.1678 47711 -
all0.17 --
obs-50106 99.968 %
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: 27.778 Å2
Baniso -1Baniso -2Baniso -3
1--1.157 Å2-0 Å20 Å2
2--1.643 Å2-0 Å2
3----0.486 Å2
Refinement stepCycle: LAST / Resolution: 1.9→71.149 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4659 0 112 321 5092
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0124975
X-RAY DIFFRACTIONr_angle_refined_deg2.5321.8376776
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2765584
X-RAY DIFFRACTIONr_dihedral_angle_2_deg8.516526
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.73110810
X-RAY DIFFRACTIONr_dihedral_angle_6_deg15.10710241
X-RAY DIFFRACTIONr_chiral_restr0.1550.2723
X-RAY DIFFRACTIONr_gen_planes_refined0.0150.023909
X-RAY DIFFRACTIONr_nbd_refined0.2220.22529
X-RAY DIFFRACTIONr_nbtor_refined0.3220.23458
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1670.2362
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2040.256
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2410.27
X-RAY DIFFRACTIONr_mcbond_it3.0672.4422321
X-RAY DIFFRACTIONr_mcangle_it3.8924.3662910
X-RAY DIFFRACTIONr_scbond_it5.4482.9022654
X-RAY DIFFRACTIONr_scangle_it7.7965.13866
X-RAY DIFFRACTIONr_lrange_it8.17228.7868071
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
1.9-1.9490.2811750.2534900.25136660.9330.9599.97270.248
1.949-2.0030.2941610.24134040.24335680.930.95599.91590.237
2.003-2.0610.2461620.2233010.22134660.9590.96499.91340.211
2.061-2.1240.2281530.1931860.19233390.9620.9751000.18
2.124-2.1940.2851530.19531280.19932810.9520.9731000.182
2.194-2.2710.2921620.18629840.19131480.9460.97599.93650.172
2.271-2.3560.241430.16829190.17230630.9660.98199.96740.154
2.356-2.4520.2541180.16628360.16929540.9550.9821000.151
2.452-2.5610.2181550.17326740.17628310.9710.98199.92940.158
2.561-2.6860.2921340.1725830.17527180.9530.98299.96320.156
2.686-2.8310.2261230.16924560.17125790.9680.9831000.155
2.831-3.0030.2041290.15823190.1624480.9750.9841000.148
3.003-3.210.2071110.16822030.1723140.9710.9821000.159
3.21-3.4660.22980.17120640.17321640.9730.98199.90760.163
3.466-3.7960.205840.1519150.15219990.9750.9871000.146
3.796-4.2430.161960.12817260.1318230.9840.99199.94510.128
4.243-4.8960.161770.1315300.13216070.9850.991000.133
4.896-5.9890.179770.1513150.15113920.980.9871000.152
5.989-8.440.173570.15710440.15811010.9850.9861000.161
8.44-71.1490.177270.1736340.1746610.9790.981000.186

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