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- PDB-9qa4: Drosophila melanogaster angiotensin converting enzyme homologue, ... -

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Basic information

Entry
Database: PDB / ID: 9qa4
TitleDrosophila melanogaster angiotensin converting enzyme homologue, AnCE in complex with WR dipeptide
Components
  • Angiotensin-converting enzyme
  • TRP-ARG 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: 1.85 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
B: TRP-ARG dipeptide
C: TRP-ARG dipeptide
A: Angiotensin-converting enzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,8469
Polymers69,8873
Non-polymers1,9596
Water13,691760
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3670 Å2
ΔGint-17 kcal/mol
Surface area24890 Å2
Unit cell
Length a, b, c (Å)172.947, 172.947, 103.007
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/peptide / Protein , 2 types, 3 molecules BCA

#1: Protein/peptide TRP-ARG dipeptide


Mass: 361.419 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Bos taurus (domestic cattle)
#2: 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

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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 , 3 types, 763 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.: 2 / Source method: obtained synthetically / Formula: C6H5O7
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 760 / 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

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: Sep 18, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95 Å / Relative weight: 1
ReflectionResolution: 1.85→86.473 Å / Num. obs: 98093 / % possible obs: 100 % / Redundancy: 10.3 % / CC1/2: 0.999 / Rpim(I) all: 0.026 / Net I/σ(I): 15.6
Reflection shellResolution: 1.85→1.88 Å / Mean I/σ(I) obs: 2.2 / Num. unique obs: 4875 / CC1/2: 0.886 / Rpim(I) all: 0.32

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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: 1.85→86.473 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.965 / SU B: 2.688 / SU ML: 0.074 / Cross valid method: FREE R-VALUE / ESU R: 0.084 / ESU R Free: 0.087
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.185 5129 5.229 %
Rwork0.1543 92961 -
all0.156 --
obs-98090 99.999 %
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: 31.852 Å2
Baniso -1Baniso -2Baniso -3
1--1.592 Å2-0.796 Å20 Å2
2---1.592 Å20 Å2
3---5.163 Å2
Refinement stepCycle: LAST / Resolution: 1.85→86.473 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4930 0 127 766 5823
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0125225
X-RAY DIFFRACTIONr_bond_other_d0.0010.0164723
X-RAY DIFFRACTIONr_angle_refined_deg1.9091.8297093
X-RAY DIFFRACTIONr_angle_other_deg0.6761.77710928
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9165600
X-RAY DIFFRACTIONr_dihedral_angle_2_deg9.091527
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.88110869
X-RAY DIFFRACTIONr_dihedral_angle_6_deg14.97110266
X-RAY DIFFRACTIONr_chiral_restr0.2390.2760
X-RAY DIFFRACTIONr_gen_planes_refined0.010.026088
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021222
X-RAY DIFFRACTIONr_nbd_refined0.2320.21140
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1830.24409
X-RAY DIFFRACTIONr_nbtor_refined0.1950.22616
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0820.22646
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1750.2623
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0330.22
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2710.28
X-RAY DIFFRACTIONr_nbd_other0.3050.253
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.150.227
X-RAY DIFFRACTIONr_mcbond_it2.6962.7882412
X-RAY DIFFRACTIONr_mcbond_other2.6972.7882412
X-RAY DIFFRACTIONr_mcangle_it3.3214.9883008
X-RAY DIFFRACTIONr_mcangle_other3.324.9893009
X-RAY DIFFRACTIONr_scbond_it4.6563.3222813
X-RAY DIFFRACTIONr_scbond_other4.6283.3212812
X-RAY DIFFRACTIONr_scangle_it6.8265.894085
X-RAY DIFFRACTIONr_scangle_other6.8265.8934086
X-RAY DIFFRACTIONr_lrange_it7.9630.9086488
X-RAY DIFFRACTIONr_lrange_other7.8629.9426210
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
1.85-1.8980.3164140.29968670.372810.8660.8721000.282
1.898-1.950.273280.26867650.26870930.9120.9221000.248
1.95-2.0070.2613330.23865340.23968670.9240.9421000.217
2.007-2.0680.2313910.20462880.20666790.9590.961000.184
2.068-2.1360.2043580.18360790.18464370.9650.9731000.165
2.136-2.2110.1923460.16459190.16662650.9760.981000.148
2.211-2.2940.1823170.15357440.15460620.9780.98499.98350.138
2.294-2.3880.1773040.14454800.14557840.9790.9861000.131
2.388-2.4940.1832680.14853080.1555760.9780.9861000.135
2.494-2.6160.1892260.14151160.14353420.9770.9881000.13
2.616-2.7570.2012650.15248270.15550920.9750.9861000.143
2.757-2.9240.2052730.16345180.16647910.9720.9841000.156
2.924-3.1260.1943720.1741160.17244880.9760.9841000.164
3.126-3.3760.1751170.1640700.1641870.9820.9881000.158
3.376-3.6980.1771890.14336620.14538510.9840.991000.143
3.698-4.1330.1491730.11233220.11334950.9880.9931000.113
4.133-4.7710.1241770.128930.10130700.9920.9951000.103
4.771-5.8380.1571300.12824900.12926200.9890.9931000.13
5.838-8.2380.1941000.14918960.15119960.9820.991000.151
8.238-86.4730.161480.15810660.15911140.9830.9811000.165

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