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

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Basic information

Entry
Database: PDB / ID: 9gbp
TitleHuman Angiotensin-1 converting enzyme N-domain in complex with a diprolyl inhibitor- SG3
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 / peptidyl-dipeptidase A / tripeptidyl-peptidase activity / 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 / peptidyl-dipeptidase A / tripeptidyl-peptidase activity / 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 / cellular response to aldosterone / hormone catabolic process / bradykinin catabolic process / angiogenesis involved in coronary vascular morphogenesis / response to thyroid hormone / negative regulation of D-glucose import / vasoconstriction / neutrophil mediated immunity / regulation of smooth muscle cell migration / 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 / heart contraction / lung alveolus development / antigen processing and presentation of peptide antigen via MHC class I / regulation of heart rate by cardiac conduction / positive regulation of systemic arterial blood pressure / response to dexamethasone / regulation of systemic arterial blood pressure by renin-angiotensin / blood vessel remodeling / hematopoietic stem cell differentiation / amyloid-beta metabolic process / regulation of vasoconstriction / peptidyl-dipeptidase activity / animal organ regeneration / angiotensin maturation / Metabolism of Angiotensinogen to Angiotensins / positive regulation of vasoconstriction / carboxypeptidase activity / 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 / lysosome / response to hypoxia / 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 / zinc ion binding / extracellular region / 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
: / ACETATE ION / DI(HYDROXYETHYL)ETHER / Angiotensin-converting enzyme
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 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)149,54930
Polymers144,9872
Non-polymers4,56328
Water15,565864
1
A: Angiotensin-converting enzyme, soluble form
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,79513
Polymers72,4931
Non-polymers2,30112
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Angiotensin-converting enzyme, soluble form
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,75517
Polymers72,4931
Non-polymers2,26116
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)73.088, 77.974, 83.312
Angle α, β, γ (deg.)88.265, 64.112, 74.362
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, 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 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 570.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-1-2/a4-b1_a6-c1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}[(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.: 4 / 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 , 9 types, 886 molecules

#4: 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.: 2 / Source method: obtained synthetically / Formula: C21H28N4O6 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#6: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#7: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H10O3
#8: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#10: Chemical ChemComp-ZN / ZINC ION


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


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


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#13: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 864 / 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: 2.92 Å3/Da / Density % sol: 57.85 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 1 M Tris/Bicine pH 8.5 60 mM divalent cations (MgCl2 and CaCl2) 30% PEG 550MME/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: Dec 1, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2→74.704 Å / Num. obs: 105007 / % possible obs: 98 % / Redundancy: 3.5 % / CC1/2: 0.996 / Rpim(I) all: 0.046 / Net I/σ(I): 10.3
Reflection shellResolution: 2→2.03 Å / Num. unique obs: 5197 / CC1/2: 0.781 / Rpim(I) all: 0.297 / % possible all: 96.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→74.704 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.933 / SU B: 4.259 / SU ML: 0.116 / Cross valid method: FREE R-VALUE / ESU R: 0.168 / ESU R Free: 0.157 / Details: Hydrogens have not been used
RfactorNum. reflection% reflection
Rfree0.2298 5130 4.886 %
Rwork0.183 99859 -
all0.185 --
obs-104989 97.959 %
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: 31.541 Å2
Baniso -1Baniso -2Baniso -3
1--0.635 Å20.758 Å20.264 Å2
2--0.566 Å20.004 Å2
3---0.442 Å2
Refinement stepCycle: LAST / Resolution: 2→74.704 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9902 0 294 864 11060
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.01210607
X-RAY DIFFRACTIONr_angle_refined_deg2.4631.83114409
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.96751224
X-RAY DIFFRACTIONr_dihedral_angle_2_deg10.852566
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.209101621
X-RAY DIFFRACTIONr_dihedral_angle_6_deg14.77210531
X-RAY DIFFRACTIONr_chiral_restr0.1650.21495
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.028424
X-RAY DIFFRACTIONr_nbd_refined0.2280.25471
X-RAY DIFFRACTIONr_nbtor_refined0.3220.27244
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1680.2936
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1950.252
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1840.216
X-RAY DIFFRACTIONr_mcbond_it4.2782.8684889
X-RAY DIFFRACTIONr_mcangle_it5.4335.1266114
X-RAY DIFFRACTIONr_scbond_it5.5493.2565718
X-RAY DIFFRACTIONr_scangle_it7.4975.7638295
X-RAY DIFFRACTIONr_lrange_it8.62833.20317276
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
2-2.0520.2863440.24172870.24378950.950.96296.65610.235
2.052-2.1080.273350.22871930.2377570.9510.96797.04780.219
2.108-2.1690.2883600.21769270.22174910.9490.9797.27670.208
2.169-2.2360.2773280.22967760.23173050.9510.96797.24850.217
2.236-2.3090.2983230.23365340.23670610.9240.95397.11090.218
2.309-2.390.2513320.18863580.19168550.960.97897.5930.177
2.39-2.480.2663440.19560660.19865520.9550.97797.83270.184
2.48-2.5810.243370.17859100.18163810.9670.98197.90.168
2.581-2.6960.2242960.17457350.17661440.9690.98298.16080.164
2.696-2.8270.2512760.17654140.1857930.9640.98198.2220.167
2.827-2.980.2432600.18451860.18755310.9640.9898.46320.175
2.98-3.160.2052440.17449180.17552320.9740.98398.66210.167
3.16-3.3780.2442490.1946100.19349200.9660.9898.76020.185
3.378-3.6480.2132210.18743350.18946110.9730.98198.80720.184
3.648-3.9960.1912180.15539230.15741780.980.98799.11440.154
3.996-4.4660.1922240.14635690.14938240.980.98799.18930.147
4.466-5.1530.1961630.14231760.14533610.9790.98999.34540.143
5.153-6.3040.2071170.16527100.16728400.9770.98699.54230.165
6.304-8.8840.246990.1920840.19221930.9750.98499.5440.192
8.884-74.7040.191600.2211480.21812240.9840.96198.69280.264

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