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- PDB-9qa1: Drosophila melanogaster angiotensin converting enzyme homologue, ... -

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Basic information

Entry
Database: PDB / ID: 9qa1
TitleDrosophila melanogaster angiotensin converting enzyme homologue, AnCE in complex with VW dipeptide
Components
  • Angiotensin-converting enzyme
  • VAL-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
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: VAL-TRP dipeptide
D: VAL-TRP dipeptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,1687
Polymers69,5873
Non-polymers1,5814
Water4,378243
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2830 Å2
ΔGint-24 kcal/mol
Surface area24840 Å2
Unit cell
Length a, b, c (Å)172.529, 172.529, 103.745
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: 68980.414 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 VAL-TRP dipeptide


Mass: 303.356 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, 244 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.: 243 / 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: 4.27 Å3/Da / Density % sol: 71.2 %
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: Oct 7, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95 Å / Relative weight: 1
ReflectionResolution: 2.2→43.17 Å / Num. obs: 58412 / % possible obs: 100 % / Redundancy: 21.7 % / CC1/2: 0.997 / Rpim(I) all: 0.07 / Net I/σ(I): 8.6
Reflection shellResolution: 2.2→2.26 Å / Mean I/σ(I) obs: 1.4 / Num. unique obs: 4498 / CC1/2: 0.824 / Rpim(I) all: 0.848

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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→43.17 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.951 / SU B: 6.02 / SU ML: 0.135 / Cross valid method: FREE R-VALUE / ESU R: 0.148 / ESU R Free: 0.145
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2115 2649 4.536 %
Rwork0.1699 55751 -
all0.172 --
obs-58400 99.914 %
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: 41.03 Å2
Baniso -1Baniso -2Baniso -3
1--2.196 Å2-1.098 Å20 Å2
2---2.196 Å20 Å2
3---7.124 Å2
Refinement stepCycle: LAST / Resolution: 2.2→43.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4909 0 101 243 5253
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0125153
X-RAY DIFFRACTIONr_bond_other_d0.0010.0164666
X-RAY DIFFRACTIONr_angle_refined_deg1.7291.8296997
X-RAY DIFFRACTIONr_angle_other_deg0.6061.77410802
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1165597
X-RAY DIFFRACTIONr_dihedral_angle_2_deg8.956524
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.66610859
X-RAY DIFFRACTIONr_dihedral_angle_6_deg14.7710262
X-RAY DIFFRACTIONr_chiral_restr0.1760.2755
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.025990
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021198
X-RAY DIFFRACTIONr_nbd_refined0.2220.21087
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1860.24227
X-RAY DIFFRACTIONr_nbtor_refined0.1920.22584
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.080.22640
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1520.2214
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0260.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.0610.28
X-RAY DIFFRACTIONr_nbd_other0.2490.239
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1630.29
X-RAY DIFFRACTIONr_mcbond_it3.0433.7162397
X-RAY DIFFRACTIONr_mcbond_other3.0423.7172398
X-RAY DIFFRACTIONr_mcangle_it4.316.6742991
X-RAY DIFFRACTIONr_mcangle_other4.316.6742992
X-RAY DIFFRACTIONr_scbond_it5.1754.3842756
X-RAY DIFFRACTIONr_scbond_other5.1744.3842757
X-RAY DIFFRACTIONr_scangle_it7.8677.7914006
X-RAY DIFFRACTIONr_scangle_other7.8667.7914007
X-RAY DIFFRACTIONr_lrange_it8.67637.8885950
X-RAY DIFFRACTIONr_lrange_other8.6837.6695917
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
2.2-2.2570.3572170.31440710.31643020.8750.89299.67460.321
2.257-2.3190.3212050.29539770.29641860.8980.91499.90440.298
2.319-2.3860.2711900.26739150.26741080.9290.93699.9270.267
2.386-2.4590.2891830.25638000.25739850.9340.94499.94980.252
2.459-2.5390.2731940.22636560.22838520.9420.96199.94810.216
2.539-2.6280.2541840.21935200.2237050.9560.96799.9730.207
2.628-2.7270.2541450.21134530.21235990.9580.97199.97220.197
2.727-2.8380.2781620.19632990.19934610.9580.9761000.181
2.838-2.9630.241190.18832010.1933200.9620.9771000.174
2.963-3.1070.2181820.17830080.1831900.9680.9811000.167
3.107-3.2740.2081690.17328250.17529940.9740.9831000.164
3.274-3.4720.2191130.1727440.17228570.9740.9851000.164
3.472-3.710.1821020.15525770.15626790.9830.9881000.151
3.71-4.0050.1551380.13923550.1424930.9880.9911000.136
4.005-4.3830.164940.11822140.11923080.9840.9921000.116
4.383-4.8940.136530.10820280.10920810.990.9931000.107
4.894-5.6390.152970.11617500.11818470.9870.9931000.116
5.639-6.8770.194560.13914960.14115520.9810.9921000.138
6.877-9.6050.183140.1212080.12112220.990.9931000.123
9.605-43.170.168320.1436540.1446910.9780.98799.27640.162

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