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- PDB-9qa3: Drosophila melanogaster angiotensin converting enzyme homologue, ... -

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Basic information

Entry
Database: PDB / ID: 9qa3
TitleDrosophila melanogaster angiotensin converting enzyme homologue, AnCE in complex with YW dipeptide
Components
  • Angiotensin-converting enzyme
  • TYR-TRP
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
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: TYR-TRP
D: TYR-TRP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,4097
Polymers69,8283
Non-polymers1,5814
Water5,513306
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3020 Å2
ΔGint-25 kcal/mol
Surface area24650 Å2
Unit cell
Length a, b, c (Å)172.432, 172.432, 103.5
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: 69093.570 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 TYR-TRP


Mass: 367.399 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: isolated from a genetically manipulated source
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: 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 , 2 types, 307 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 306 / 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: 4.24 Å3/Da / Density % sol: 71 %
Crystal growTemperature: 289 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: Dec 15, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95 Å / Relative weight: 1
ReflectionResolution: 2.2→86.22 Å / Num. obs: 58227 / % possible obs: 100 % / Redundancy: 10.2 % / CC1/2: 0.994 / Rpim(I) all: 0.077 / Net I/σ(I): 7
Reflection shellResolution: 2.2→2.26 Å / Mean I/σ(I) obs: 1.8 / Num. unique obs: 4478 / CC1/2: 0.599 / Rpim(I) all: 0.692

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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→86.216 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.95 / SU B: 6.159 / SU ML: 0.139 / Cross valid method: FREE R-VALUE / ESU R: 0.144 / ESU R Free: 0.143
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2058 2789 4.79 %
Rwork0.1628 55434 -
all0.165 --
obs-58223 99.995 %
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: 36.774 Å2
Baniso -1Baniso -2Baniso -3
1--1.063 Å2-0.532 Å20 Å2
2---1.063 Å2-0 Å2
3---3.449 Å2
Refinement stepCycle: LAST / Resolution: 2.2→86.216 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4928 0 101 306 5335
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0125174
X-RAY DIFFRACTIONr_bond_other_d0.0010.0164675
X-RAY DIFFRACTIONr_angle_refined_deg2.561.837026
X-RAY DIFFRACTIONr_angle_other_deg0.861.77410823
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.645598
X-RAY DIFFRACTIONr_dihedral_angle_2_deg10.79524
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.05610861
X-RAY DIFFRACTIONr_dihedral_angle_6_deg15.36210264
X-RAY DIFFRACTIONr_chiral_restr0.2350.2755
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.026017
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021207
X-RAY DIFFRACTIONr_nbd_refined0.2340.21193
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2040.24557
X-RAY DIFFRACTIONr_nbtor_refined0.2050.22638
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0960.22793
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1590.2271
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0640.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1920.211
X-RAY DIFFRACTIONr_nbd_other0.2480.248
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1710.26
X-RAY DIFFRACTIONr_mcbond_it3.8873.2972401
X-RAY DIFFRACTIONr_mcbond_other3.8873.2972402
X-RAY DIFFRACTIONr_mcangle_it5.0525.8992996
X-RAY DIFFRACTIONr_mcangle_other5.0525.8992997
X-RAY DIFFRACTIONr_scbond_it6.573.9262773
X-RAY DIFFRACTIONr_scbond_other6.573.9262774
X-RAY DIFFRACTIONr_scangle_it8.9736.9294030
X-RAY DIFFRACTIONr_scangle_other8.9726.9294031
X-RAY DIFFRACTIONr_lrange_it9.6132.8466146
X-RAY DIFFRACTIONr_lrange_other9.6332.7486113
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
2.2-2.2570.3082110.28440480.28542590.9210.931000.267
2.257-2.3190.291600.26640390.26741990.930.941000.249
2.319-2.3860.3081710.24839310.25141020.9170.9491000.229
2.386-2.460.2572290.23937520.2439810.9480.9541000.22
2.46-2.540.2622390.22336040.22538430.940.9631000.204
2.54-2.6290.2651590.21735560.21937150.9520.9681000.199
2.629-2.7280.2641700.20534110.20835820.9530.97299.97210.188
2.728-2.840.2521660.19633020.19834680.9620.9751000.181
2.84-2.9660.2421460.1931390.19232850.9610.9771000.176
2.966-3.110.2771100.18230670.18531770.9480.981000.172
3.11-3.2780.2161230.16729030.16930260.9680.9831000.163
3.278-3.4770.1951190.1527010.15228200.980.9881000.148
3.477-3.7170.1921620.13825050.14126680.980.9999.96250.139
3.717-4.0140.171980.11924130.12125110.9850.9931000.124
4.014-4.3960.1381460.10121520.10322980.9890.9941000.109
4.396-4.9130.1511100.09919420.10120520.9870.9951000.108
4.913-5.670.152690.11217540.11418230.9890.9941000.122
5.67-6.9370.1891150.12914400.13415550.9820.9921000.139
6.937-9.7790.128820.10811070.1111890.990.9941000.124
9.779-86.2160.20440.1436680.1446730.970.98799.85140.167

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