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- PDB-9qam: Human angiotensin-1 converting enzyme C-domain in complex with ci... -

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Basic information

Entry
Database: PDB / ID: 9qam
TitleHuman angiotensin-1 converting enzyme C-domain in complex with ciprofloxacin
ComponentsAngiotensin-converting enzyme, soluble form
KeywordsHYDROLASE / Inhibitor / complex / antibiotic / ciprofloxacin / hypertension
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 / antigen processing and presentation of peptide antigen via MHC class I / regulation of heart rate by cardiac conduction / 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
Chem-CPF / IMIDAZOLE / MALONATE ION / N-CARBOXYALANINE / DI(HYDROXYETHYL)ETHER / Angiotensin-converting enzyme
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsGregory, K.S. / Acharya, K.R.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)BB/X001032/1 United Kingdom
CitationJournal: Acs Bio Med Chem Au / Year: 2025
Title: Ciprofloxacin Inhibits Angiotensin I‐Converting Enzyme (ACE) Activity by Binding at the Exosite, Distal to the Catalytic Pocket.
Authors: Gregory, K.S. / Ramasamy, V. / Sturrock, E.D. / Acharya, K.R.
History
DepositionFeb 28, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 12, 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, soluble form
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,03514
Polymers66,7641
Non-polymers2,27113
Water5,981332
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4020 Å2
ΔGint-27 kcal/mol
Surface area23130 Å2
Unit cell
Length a, b, c (Å)60.087, 85.417, 135.662
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, soluble form


Mass: 66763.578 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

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Sugars , 2 types, 2 molecules

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


Type: oligosaccharide / Mass: 570.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-1-2/a4-b1_a6-c1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}[(6+1)][a-L-Fucp]{}}LINUCSPDB-CARE
#3: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-3)-1-deoxy-alpha-D-mannopyranose


Type: oligosaccharide / Mass: 367.349 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
WURCS=2.0/2,2,1/[h1122h_2-6][a2122h-1b_1-5_2*NCC/3=O]/1-2/a4-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-Manp]{[(3+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE

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Non-polymers , 9 types, 343 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
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H5N2
#7: Chemical ChemComp-NXA / N-CARBOXYALANINE


Mass: 133.103 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H7NO4
#8: Chemical ChemComp-MLI / MALONATE ION


Mass: 102.046 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H2O4
#9: Chemical ChemComp-CPF / 1-CYCLOPROPYL-6-FLUORO-4-OXO-7-PIPERAZIN-1-YL-1,4-DIHYDROQUINOLINE-3-CARBOXYLIC ACID / ciprofloxacin


Mass: 331.342 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H18FN3O3 / Feature type: SUBJECT OF INVESTIGATION
#10: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#11: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#12: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 332 / 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: 2.64 Å3/Da / Density % sol: 53.41 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 4 / Details: 0.1 M MIB pH 4.0, 5% glycerol, 15% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.953731 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 23, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.953731 Å / Relative weight: 1
ReflectionResolution: 1.85→135.66 Å / Num. obs: 60479 / % possible obs: 100 % / Redundancy: 13.4 % / CC1/2: 0.995 / Rpim(I) all: 0.067 / Net I/σ(I): 6.7
Reflection shellResolution: 1.85→1.89 Å / Num. unique obs: 3683 / CC1/2: 0.63 / Rpim(I) all: 0.712

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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→72.387 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.948 / SU B: 8.711 / SU ML: 0.123 / Cross valid method: FREE R-VALUE / ESU R: 0.141 / ESU R Free: 0.128
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2268 3064 5.073 %
Rwork0.1986 57332 -
all0.2 --
obs-60396 99.987 %
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: 35.104 Å2
Baniso -1Baniso -2Baniso -3
1-2.726 Å20 Å2-0 Å2
2---2.218 Å20 Å2
3----0.508 Å2
Refinement stepCycle: LAST / Resolution: 1.85→72.387 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4649 0 150 332 5131
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0125010
X-RAY DIFFRACTIONr_bond_other_d0.0010.0164561
X-RAY DIFFRACTIONr_angle_refined_deg1.7861.8186821
X-RAY DIFFRACTIONr_angle_other_deg0.6091.75810530
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4775583
X-RAY DIFFRACTIONr_dihedral_angle_2_deg8.2336.07128
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.63610808
X-RAY DIFFRACTIONr_dihedral_angle_6_deg15.19310.083242
X-RAY DIFFRACTIONr_chiral_restr0.1710.2718
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.025907
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021187
X-RAY DIFFRACTIONr_nbd_refined0.2320.21136
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1860.24146
X-RAY DIFFRACTIONr_nbtor_refined0.1890.22466
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0770.22419
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1790.2277
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.190.215
X-RAY DIFFRACTIONr_nbd_other0.1880.235
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1790.214
X-RAY DIFFRACTIONr_mcbond_it1.7732.0492320
X-RAY DIFFRACTIONr_mcbond_other1.7692.0492320
X-RAY DIFFRACTIONr_mcangle_it2.6593.6722907
X-RAY DIFFRACTIONr_mcangle_other2.663.6722908
X-RAY DIFFRACTIONr_scbond_it2.5622.4292690
X-RAY DIFFRACTIONr_scbond_other2.5622.4312691
X-RAY DIFFRACTIONr_scangle_it4.0064.3443908
X-RAY DIFFRACTIONr_scangle_other4.0054.3453909
X-RAY DIFFRACTIONr_lrange_it5.91222.0265936
X-RAY DIFFRACTIONr_lrange_other5.83421.5185854
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
1.85-1.8980.3172100.33642150.33544270.8930.89399.95480.342
1.898-1.950.3082230.31340610.31342840.9050.9071000.317
1.95-2.0060.32340.2939520.29141860.9260.9321000.293
2.006-2.0680.2741850.24638530.24840380.9410.9531000.244
2.068-2.1360.2761840.23337870.23539710.9380.9591000.229
2.136-2.2110.2321800.20936110.2137920.9640.96999.97360.203
2.211-2.2940.2331850.21534990.21636840.9610.9661000.208
2.294-2.3880.2622100.18933560.19335670.9560.97699.9720.178
2.388-2.4940.2261690.1832300.18333990.970.981000.171
2.494-2.6150.2331950.17930880.18232840.9650.9899.96960.168
2.615-2.7570.2291560.17129590.17431150.9670.9811000.162
2.757-2.9240.2281560.18327850.18529410.9650.9791000.173
2.924-3.1250.2581510.19426390.19727910.9590.97799.96420.186
3.125-3.3750.2481170.1924920.19326090.9640.9811000.184
3.375-3.6960.2161170.19922890.224060.9740.9791000.193
3.696-4.1310.2990.16820820.16921810.9760.9831000.166
4.131-4.7680.165970.15318640.15419610.9820.9871000.152
4.768-5.8330.185810.17515700.17516510.9810.9861000.175
5.833-8.2230.197770.18112480.18213250.9790.9821000.181
8.223-72.3870.165380.237520.2267920.9820.9599.74750.231
Refinement TLS params.Method: refined / Origin x: -13.2323 Å / Origin y: 1.6574 Å / Origin z: -25.2427 Å
111213212223313233
T0.0608 Å20.0242 Å20.0078 Å2-0.0391 Å2-0.005 Å2--0.0166 Å2
L0.833 °20.0541 °2-0.0692 °2-1.3526 °2-0.204 °2--1.204 °2
S-0.0689 Å °-0.1226 Å °0.0344 Å °0.1815 Å °0.0539 Å °0.131 Å °-0.0195 Å °-0.1401 Å °0.015 Å °
Refinement TLS groupSelection: ALL

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