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

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Basic information

Entry
Database: PDB / ID: 9gbn
TitleHuman Angiotensin-1 converting enzyme C-domain in complex with a diprolyl inhibitor- SG15
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 / positive regulation of systemic arterial blood pressure / regulation of heart rate by cardiac conduction / antigen processing and presentation of peptide antigen via MHC class I / regulation of systemic arterial blood pressure by renin-angiotensin / blood vessel remodeling / amyloid-beta metabolic process / hematopoietic stem cell differentiation / peptidyl-dipeptidase activity / regulation of vasoconstriction / 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
: / 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,2058
Polymers68,8621
Non-polymers2,3437
Water6,017334
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2850 Å2
ΔGint14 kcal/mol
Surface area24120 Å2
Unit cell
Length a, b, c (Å)56.356, 84.229, 133.728
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 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[2-acetamido-2-deoxy- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)]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: 1463.349 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-2DManpa1-3[DGlcpNAcb1-2DManpa1-6]DManpb1-4DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/4,8,7/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5][a1221m-1a_1-5]/1-1-2-3-1-3-1-4/a4-b1_a6-h1_b4-c1_c3-d1_c6-f1_d2-e1_f2-g1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{[(2+1)][b-D-GlcpNAc]{}}[(6+1)][a-D-Manp]{[(2+1)][b-D-GlcpNAc]{}}}}[(6+1)][a-L-Fucp]{}}LINUCSPDB-CARE
#3: 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 , 5 types, 339 molecules

#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#7: Chemical ChemComp-A1IJZ / (2S)-1-[(2S)-2-[[(1S)-1-[(2S)-1-[(2S)-2-azanyl-3-phenyl-propanoyl]pyrrolidin-2-yl]-2-oxidanyl-2-oxidanylidene-ethyl]amino]propanoyl]pyrrolidine-2-carboxylic acid


Mass: 460.523 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C23H32N4O6 / Feature type: SUBJECT OF INVESTIGATION
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 334 / 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: 2.38 Å3/Da / Density % sol: 48.4 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, sitting drop / 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: I04-1 / Wavelength: 0.9119 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Feb 2, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9119 Å / Relative weight: 1
ReflectionResolution: 2→133.73 Å / Num. obs: 43891 / % possible obs: 100 % / Redundancy: 10.9 % / CC1/2: 0.997 / Rpim(I) all: 0.064 / Net I/σ(I): 7.9
Reflection shellResolution: 2→2.05 Å / Num. unique obs: 3184 / CC1/2: 0.556 / Rpim(I) all: 0.477 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→71.372 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.932 / SU B: 11.235 / SU ML: 0.134 / Cross valid method: FREE R-VALUE / ESU R: 0.181 / ESU R Free: 0.167 / Details: Hydrogens have not been used
RfactorNum. reflection% reflection
Rfree0.2319 2153 4.915 %
Rwork0.1779 41656 -
all0.181 --
obs-43809 99.911 %
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: 33.852 Å2
Baniso -1Baniso -2Baniso -3
1--0.264 Å2-0 Å2-0 Å2
2---0.666 Å20 Å2
3---0.93 Å2
Refinement stepCycle: LAST / Resolution: 2→71.372 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4693 0 153 334 5180
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0125011
X-RAY DIFFRACTIONr_angle_refined_deg2.6081.846826
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0915577
X-RAY DIFFRACTIONr_dihedral_angle_2_deg7.579526
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.00810807
X-RAY DIFFRACTIONr_dihedral_angle_6_deg15.16410242
X-RAY DIFFRACTIONr_chiral_restr0.1660.2741
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.023892
X-RAY DIFFRACTIONr_nbd_refined0.2310.22622
X-RAY DIFFRACTIONr_nbtor_refined0.3310.23506
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1740.2393
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2050.262
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2560.219
X-RAY DIFFRACTIONr_mcbond_it2.522.0642311
X-RAY DIFFRACTIONr_mcangle_it3.5263.692887
X-RAY DIFFRACTIONr_scbond_it4.1792.5212700
X-RAY DIFFRACTIONr_scangle_it5.8284.4773939
X-RAY DIFFRACTIONr_lrange_it7.01125.1528227
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
2-2.0520.3151540.27130080.27331800.9260.94399.4340.271
2.052-2.1080.3071420.24629890.24831310.9330.9561000.245
2.108-2.1690.2891460.22628970.22930430.9410.9631000.221
2.169-2.2360.2811420.21727570.2229000.9480.96799.96550.21
2.236-2.3090.2561330.21127410.21328750.9580.96999.96520.2
2.309-2.390.2341330.20326260.20527600.9630.97299.96380.19
2.39-2.480.2491230.17925580.18226810.9630.9791000.166
2.48-2.5810.2571470.18924310.19325790.9580.97799.96120.172
2.581-2.6960.2231250.17623540.17824800.970.98199.95970.16
2.696-2.8270.2481080.17822660.18123750.9680.98199.95790.161
2.827-2.980.2431300.17921310.18322610.960.981000.163
2.98-3.160.2681100.18220350.18621450.9530.981000.167
3.16-3.3780.2131090.17319090.17620190.9730.98299.95050.163
3.378-3.6480.251870.17817990.18118860.9620.9821000.168
3.648-3.9950.201910.14716620.1517540.9780.98899.9430.14
3.995-4.4650.166750.14615040.14715790.9850.9881000.139
4.465-5.1520.199610.12913610.13214220.9780.991000.124
5.152-6.3020.206630.14811580.15112210.9710.9881000.142
6.302-8.8770.193470.1469160.1489630.9830.9891000.143
8.877-71.3720.197270.1965540.1975820.9790.97599.82820.194
Refinement TLS params.Method: refined / Origin x: -12.5619 Å / Origin y: -5.2183 Å / Origin z: 23.5048 Å
111213212223313233
T0.0288 Å2-0.0229 Å2-0.0057 Å2-0.0384 Å2-0.0046 Å2--0.0148 Å2
L0.9801 °2-0.0146 °2-0.0202 °2-0.9227 °2-0.4917 °2--1.0518 °2
S-0.0601 Å °0.1669 Å °-0.0524 Å °-0.131 Å °0.0749 Å °0.0889 Å °0.0679 Å °-0.0934 Å °-0.0147 Å °
Refinement TLS groupSelection: ALL

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