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- PDB-9qa0: Drosophila melanogaster angiotensin converting enzyme homologue, ... -

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Basic information

Entry
Database: PDB / ID: 9qa0
TitleDrosophila melanogaster angiotensin converting enzyme homologue, AnCE in complex with IW dipeptide
Components
  • Angiotensin-converting enzyme
  • ILE-TRP dipeptide
KeywordsHYDROLASE / metalloprotease / dipeptides / hypertension
Function / homology
Function and homology information


Metabolism of Angiotensinogen to Angiotensins / metamorphosis / response to symbiotic bacterium / peptidyl-dipeptidase A / sexual reproduction / peptide hormone processing / peptidyl-dipeptidase activity / carboxypeptidase activity / metallopeptidase activity / proteolysis ...Metabolism of Angiotensinogen to Angiotensins / metamorphosis / response to symbiotic bacterium / peptidyl-dipeptidase A / sexual reproduction / peptide hormone processing / peptidyl-dipeptidase activity / carboxypeptidase activity / metallopeptidase activity / proteolysis / extracellular space / metal 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
CITRATE ANION / Angiotensin-converting enzyme
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
Bos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsZukowska, J. / Gregory, K.S. / Acharya, K.R.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
UK Research and Innovation (UKRI)BB/X001032/1 United Kingdom
CitationJournal: Biomolecules / Year: 2025
Title: Molecular Basis of Dipeptide Recognition in Drosophila melanogaster Angiotensin I-Converting Enzyme Homologue, AnCE.
Authors: Zukowska, J. / Gregory, K.S. / Robinson, A. / Isaac, R.E. / Acharya, K.R.
History
DepositionFeb 27, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 14, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Angiotensin-converting enzyme
B: ILE-TRP dipeptide
D: ILE-TRP dipeptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,5698
Polymers69,7993
Non-polymers1,7705
Water4,252236
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)173.236, 173.236, 103.069
Angle α, β, γ (deg.)90, 90, 120
Int Tables number146
Space group name H-MH3

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Components

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Protein / Protein/peptide , 2 types, 3 molecules ABD

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


Mass: 69164.656 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: Ance, Race, CG8827 / Production host: Komagataella phaffii GS115 (fungus) / References: UniProt: Q10714, peptidyl-dipeptidase A
#2: Protein/peptide ILE-TRP dipeptide


Mass: 317.383 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Bos taurus (domestic cattle)

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Sugars , 2 types, 3 molecules

#3: Polysaccharide beta-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D- ...beta-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1072.964 Da / Num. of mol.: 1 / Source method: obtained synthetically
DescriptorTypeProgram
DManpb1-6DManpa1-3[DManpa1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,6,5/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-2-3/a4-b1_b4-c1_c3-d1_c6-f1_d6-e1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{[(6+1)][b-D-Manp]{}}[(6+1)][a-D-Manp]{}}}}LINUCSPDB-CARE
#5: 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.: 2 / Source method: isolated from a natural source / 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 , 3 types, 238 molecules

#4: 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-FLC / CITRATE ANION


Mass: 189.100 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C6H5O7
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 236 / 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: 4.26 Å3/Da / Density % sol: 71.16 %
Crystal growTemperature: 299 K / Method: vapor diffusion, hanging drop / Details: 1.2 M sodium citrate, 0.1 M HEPES pH 7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.95 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Nov 14, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95 Å / Relative weight: 1
ReflectionResolution: 2.2→50.059 Å / Num. obs: 58565 / % possible obs: 100 % / Redundancy: 10.6 % / CC1/2: 0.997 / Rpim(I) all: 0.062 / Net I/σ(I): 8.3
Reflection shellResolution: 2.2→2.26 Å / Mean I/σ(I) obs: 1.3 / Num. unique obs: 4567 / CC1/2: 0.704 / Rpim(I) all: 0.572 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0430 (refmacat 0.4.100)refinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→50.059 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.955 / WRfactor Rfree: 0.183 / WRfactor Rwork: 0.148 / Average fsc free: 0.9519 / Average fsc work: 0.9646 / Cross valid method: FREE R-VALUE / ESU R: 0.15 / ESU R Free: 0.144
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2082 3107 5.306 %
Rwork0.1705 55451 -
all0.173 --
obs-58558 99.993 %
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: 41.428 Å2
Baniso -1Baniso -2Baniso -3
1--1.561 Å2-0.781 Å20 Å2
2---1.561 Å20 Å2
3---5.064 Å2
Refinement stepCycle: LAST / Resolution: 2.2→50.059 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4924 0 114 236 5274
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0125180
X-RAY DIFFRACTIONr_bond_other_d00.0164690
X-RAY DIFFRACTIONr_angle_refined_deg2.4631.8287034
X-RAY DIFFRACTIONr_angle_other_deg0.8161.77410858
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4575599
X-RAY DIFFRACTIONr_dihedral_angle_2_deg8.07524
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.37710863
X-RAY DIFFRACTIONr_dihedral_angle_6_deg14.90510262
X-RAY DIFFRACTIONr_chiral_restr0.1150.2759
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.026016
X-RAY DIFFRACTIONr_gen_planes_other0.0240.021200
X-RAY DIFFRACTIONr_nbd_refined0.2330.21174
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2150.24338
X-RAY DIFFRACTIONr_nbtor_refined0.2010.22590
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0950.22723
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1510.2208
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.0940.26
X-RAY DIFFRACTIONr_nbd_other0.2280.243
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2060.23
X-RAY DIFFRACTIONr_mcbond_it4.3143.7152405
X-RAY DIFFRACTIONr_mcbond_other4.3143.7152405
X-RAY DIFFRACTIONr_mcangle_it5.5576.6623001
X-RAY DIFFRACTIONr_mcangle_other5.5566.6623002
X-RAY DIFFRACTIONr_scbond_it7.0764.4272775
X-RAY DIFFRACTIONr_scbond_other7.0744.4272776
X-RAY DIFFRACTIONr_scangle_it9.737.8424033
X-RAY DIFFRACTIONr_scangle_other9.7297.8424034
X-RAY DIFFRACTIONr_lrange_it10.23736.256025
X-RAY DIFFRACTIONr_lrange_other10.23736.2496026
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
2.2-2.2570.3422390.32141150.32243540.880.8981000.32
2.257-2.3190.2822330.2939660.2941990.9380.9261000.288
2.319-2.3860.2971980.28239080.28341060.9130.9341000.276
2.386-2.4590.3042510.2637410.26339930.920.94499.9750.252
2.459-2.540.2951990.22936510.23238500.9390.9611000.218
2.54-2.6290.2871800.22335500.22637300.9480.9671000.208
2.629-2.7270.2611370.20934460.21135830.9580.9721000.194
2.727-2.8380.2371580.20133400.20334980.9640.9741000.184
2.838-2.9640.2461980.19231030.19533010.9610.9771000.176
2.964-3.1080.262060.19229980.19732040.9590.9771000.178
3.108-3.2760.2141300.1828630.18129930.9710.9821000.171
3.276-3.4740.2151470.17127330.17428800.9740.9851000.163
3.474-3.7120.1931200.16325420.16426620.9770.9881000.155
3.712-4.0080.1811160.13624000.13825160.9810.9921000.13
4.008-4.3870.1331490.10321590.10523080.990.9941000.097
4.387-4.9010.1571430.10619450.10920880.9860.9941000.099
4.901-5.650.141800.10717490.10818290.9890.9951000.101
5.65-6.8980.173720.12914890.13215610.9860.9921000.123
6.898-9.6630.153870.11311300.11612170.9860.9941000.106
9.663-50.0590.156640.1316230.1336870.9880.9891000.118

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