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- PDB-8qfx: Human Angiotensin-1 converting enzyme N-domain in complex with th... -

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Basic information

Entry
Database: PDB / ID: 8qfx
TitleHuman Angiotensin-1 converting enzyme N-domain in complex with the lactotripeptide IPP
Components
  • Angiotensin-converting enzyme, soluble form
  • ILE-PRO-PRO
KeywordsHYDROLASE / inhibitor / complex / angiotensin I coverting enzyme / metalloprotease / lactotripeptide
Function / homology
Function and homology information


mononuclear cell proliferation / cell proliferation in bone marrow / bradykinin receptor binding / regulation of angiotensin metabolic process / exopeptidase activity / substance P catabolic process / peptidyl-dipeptidase A / tripeptidyl-peptidase activity / regulation of renal output by angiotensin / negative regulation of calcium ion import ...mononuclear cell proliferation / cell proliferation in bone marrow / bradykinin receptor binding / regulation of angiotensin metabolic process / exopeptidase activity / substance P catabolic process / peptidyl-dipeptidase A / tripeptidyl-peptidase activity / regulation of renal output by angiotensin / negative regulation of calcium ion import / positive regulation of peptidyl-cysteine S-nitrosylation / response to laminar fluid shear stress / negative regulation of gap junction assembly / metallodipeptidase activity / positive regulation of systemic arterial blood pressure / cellular response to aldosterone / hormone catabolic process / bradykinin catabolic process / angiogenesis involved in coronary vascular morphogenesis / response to thyroid hormone / antigen processing and presentation of peptide antigen via MHC class I / negative regulation of glucose import / vasoconstriction / hormone metabolic process / neutrophil mediated immunity / regulation of smooth muscle cell migration / regulation of hematopoietic stem cell proliferation / mitogen-activated protein kinase binding / embryo development ending in birth or egg hatching / chloride ion binding / mitogen-activated protein kinase kinase binding / positive regulation of neurogenesis / arachidonic acid secretion / post-transcriptional regulation of gene expression / eating behavior / heterocyclic compound binding / lung alveolus development / heart contraction / peptide catabolic process / response to dexamethasone / regulation of heart rate by cardiac conduction / regulation of systemic arterial blood pressure by renin-angiotensin / regulation of vasoconstriction / peptidyl-dipeptidase activity / hematopoietic stem cell differentiation / blood vessel remodeling / angiotensin maturation / amyloid-beta metabolic process / animal organ regeneration / Metabolism of Angiotensinogen to Angiotensins / carboxypeptidase activity / positive regulation of vasoconstriction / sperm midpiece / blood vessel diameter maintenance / response to nutrient levels / basal plasma membrane / kidney development / angiotensin-activated signaling pathway / female pregnancy / cellular response to glucose stimulus / brush border membrane / regulation of synaptic plasticity / metalloendopeptidase activity / regulation of blood pressure / metallopeptidase activity / male gonad development / peptidase activity / actin binding / spermatogenesis / endopeptidase activity / response to lipopolysaccharide / lysosome / calmodulin binding / response to hypoxia / endosome / response to xenobiotic stimulus / positive regulation of apoptotic process / external side of plasma membrane / negative regulation of gene expression / proteolysis / extracellular space / zinc ion binding / extracellular exosome / extracellular region / plasma membrane
Similarity search - Function
Peptidase family M2 domain profile. / Peptidase M2, peptidyl-dipeptidase A / Angiotensin-converting enzyme / Neutral zinc metallopeptidases, zinc-binding region signature.
Similarity search - Domain/homology
ACETATE ION / beta-D-mannopyranose / alpha-L-fucopyranose / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / Angiotensin-converting enzyme
Similarity search - Component
Biological speciesHomo sapiens (human)
Bos taurus (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsGregory, K.S. / Acharya, K.R. / Cozier, G.E.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)BB/X001032/1 United Kingdom
CitationJournal: Febs Lett. / Year: 2024
Title: Structural insights into the inhibitory mechanism of angiotensin-I-converting enzyme by the lactotripeptides IPP and VPP.
Authors: Gregory, K.S. / Cozier, G.E. / Schwager, S.L.U. / Sturrock, E.D. / Acharya, K.R.
History
DepositionSep 5, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 22, 2023Provider: repository / Type: Initial release
Revision 1.1Feb 7, 2024Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year

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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
B: Angiotensin-converting enzyme, soluble form
C: Angiotensin-converting enzyme, soluble form
D: Angiotensin-converting enzyme, soluble form
E: ILE-PRO-PRO
F: ILE-PRO-PRO
G: ILE-PRO-PRO
H: ILE-PRO-PRO
hetero molecules


Theoretical massNumber of molelcules
Total (without water)303,89289
Polymers291,2758
Non-polymers12,61781
Water41,8852325
1
A: Angiotensin-converting enzyme, soluble form
G: ILE-PRO-PRO
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,78425
Polymers72,8192
Non-polymers3,96523
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6770 Å2
ΔGint-7 kcal/mol
Surface area26710 Å2
MethodPISA
2
B: Angiotensin-converting enzyme, soluble form
F: ILE-PRO-PRO
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,40421
Polymers72,8192
Non-polymers2,58619
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6700 Å2
ΔGint-6 kcal/mol
Surface area26130 Å2
MethodPISA
3
C: Angiotensin-converting enzyme, soluble form
E: ILE-PRO-PRO
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,78421
Polymers72,8192
Non-polymers2,96519
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5580 Å2
ΔGint-21 kcal/mol
Surface area25430 Å2
MethodPISA
4
D: Angiotensin-converting enzyme, soluble form
H: ILE-PRO-PRO
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,92022
Polymers72,8192
Non-polymers3,10120
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4210 Å2
ΔGint-35 kcal/mol
Surface area25090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.229, 103.395, 115.416
Angle α, β, γ (deg.)84.950, 85.493, 81.549
Int Tables number1
Space group name H-MP1

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Components

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Protein / Protein/peptide , 2 types, 8 molecules ABCDEFGH

#1: Protein
Angiotensin-converting enzyme, soluble form


Mass: 72493.352 Da / Num. of mol.: 4
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
#2: Protein/peptide
ILE-PRO-PRO


Mass: 325.403 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) Bos taurus (cattle)

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Sugars , 6 types, 26 molecules

#3: Polysaccharide
alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 367.349 Da / Num. of mol.: 4 / Source method: obtained synthetically
DescriptorTypeProgram
LFucpa1-6DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-2/a6-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(6+1)][a-L-Fucp]{}}LINUCSPDB-CARE
#4: 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: obtained synthetically
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
#5: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 2 / Source method: obtained synthetically
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE
#14: 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.: 13 / 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
#15: Sugar
ChemComp-BMA / beta-D-mannopyranose / beta-D-mannose / D-mannose / mannose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: C6H12O6
IdentifierTypeProgram
DManpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-mannopyranoseCOMMON NAMEGMML 1.0
b-D-ManpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
ManSNFG CARBOHYDRATE SYMBOLGMML 1.0
#17: Sugar ChemComp-FUC / alpha-L-fucopyranose / alpha-L-fucose / 6-deoxy-alpha-L-galactopyranose / L-fucose / fucose


Type: L-saccharide, alpha linking / Mass: 164.156 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H12O5
IdentifierTypeProgram
LFucpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-L-fucopyranoseCOMMON NAMEGMML 1.0
a-L-FucpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
FucSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 12 types, 2380 molecules

#6: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: Cl / Feature type: SUBJECT OF INVESTIGATION
#8: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#9: Chemical
ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C6H14O4
#10: Chemical ChemComp-12P / DODECAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400


Mass: 546.646 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H50O13 / Comment: precipitant*YM
#11: Chemical ChemComp-XPE / 3,6,9,12,15,18,21,24,27-NONAOXANONACOSANE-1,29-DIOL / DECAETHYLENE GLYCOL


Mass: 458.541 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H42O11 / Comment: precipitant*YM
#12: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 11 / Source method: isolated from a natural source / Formula: C4H10O3
#13: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: C2H6O2
#16: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#18: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C8H18O5 / Comment: precipitant*YM
#19: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#20: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2325 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 3.06 Å3/Da / Density % sol: 59.78 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 30% PEG 500 MME/PEG 20000, 0.1 M Tris/Bicine pH 8.5 and 60 mM divalent cations [Molecular Dimensions (Rotherham, UK) Morpheus A9]

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9282 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Dec 17, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9282 Å / Relative weight: 1
ReflectionResolution: 1.6→114.71 Å / Num. obs: 432760 / % possible obs: 97.2 % / Redundancy: 6.9 % / CC1/2: 0.998 / Rpim(I) all: 0.061 / Net I/σ(I): 6.4
Reflection shellResolution: 1.6→1.63 Å / Num. unique obs: 20957 / CC1/2: 0.344 / Rpim(I) all: 0.859

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Processing

Software
NameVersionClassification
REFMAC5.8.0419refinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→79.452 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.957 / SU B: 4.187 / SU ML: 0.071 / Cross valid method: FREE R-VALUE / ESU R: 0.081 / ESU R Free: 0.083
RfactorNum. reflection% reflection
Rfree0.2109 21616 4.995 %
Rwork0.1808 411119 -
all0.182 --
obs-432735 97.142 %
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: 24.203 Å2
Baniso -1Baniso -2Baniso -3
1--0.631 Å2-0.106 Å2-0.207 Å2
2--0.338 Å2-0.067 Å2
3---0.206 Å2
Refinement stepCycle: LAST / Resolution: 1.6→79.452 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19974 0 800 2329 23103
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.01221998
X-RAY DIFFRACTIONr_angle_refined_deg1.9391.66929931
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.21752575
X-RAY DIFFRACTIONr_dihedral_angle_2_deg8.2175137
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.876103357
X-RAY DIFFRACTIONr_dihedral_angle_6_deg16.383101091
X-RAY DIFFRACTIONr_chiral_restr0.1340.23122
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.0217460
X-RAY DIFFRACTIONr_nbd_refined0.2350.29320
X-RAY DIFFRACTIONr_nbtor_refined0.3090.214586
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2090.21484
X-RAY DIFFRACTIONr_metal_ion_refined0.0890.23
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2680.2123
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1710.258
X-RAY DIFFRACTIONr_mcbond_it1.4531.22510111
X-RAY DIFFRACTIONr_mcangle_it2.1372.19912732
X-RAY DIFFRACTIONr_scbond_it2.9341.64811887
X-RAY DIFFRACTIONr_scangle_it4.2922.86417194
X-RAY DIFFRACTIONr_lrange_it6.40617.40633009
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
1.6-1.6410.35415910.338297640.339329950.9110.91895.02950.336
1.641-1.6860.30515190.301292650.301321040.9320.93595.88840.301
1.686-1.7350.29114510.271285730.272311970.9410.94996.240.273
1.735-1.7890.27515020.25277210.251303330.950.95896.34060.25
1.789-1.8470.26913610.231269770.233294090.9550.96696.35830.229
1.847-1.9120.25113540.215261660.217284370.9610.97196.77530.212
1.912-1.9840.22413500.2251030.201273550.9680.97596.70260.193
1.984-2.0650.22213320.189243750.19265040.9680.97896.99290.18
2.065-2.1570.22211930.176234030.178252760.970.98197.30970.167
2.157-2.2620.20412100.166223940.168242100.9740.98497.49690.157
2.262-2.3840.19611480.16213140.162229730.9760.96497.77570.151
2.384-2.5290.19210670.156202070.158217450.9770.98597.8340.149
2.529-2.7030.2059630.162191560.164204510.9750.98498.37660.154
2.703-2.920.1999510.166177720.168190020.9760.98498.53170.158
2.92-3.1980.2048810.17164570.172175620.9760.98398.72450.163
3.198-3.5750.1937540.166148950.167158540.9780.98598.70690.16
3.575-4.1260.1557370.133131100.134139880.9870.9998.9920.128
4.126-5.050.1615830.131110740.132117740.9870.99199.00630.127
5.05-7.1280.1984550.16885760.1791090.9810.98799.14370.166
7.128-79.4520.1912140.17848170.17850480.9810.98399.66320.172
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.8348-0.05270.1410.73360.15970.5640.02970.0791-0.08430.0089-0.0061-0.04050.0110.0393-0.02360.0276-0.0045-0.01110.0121-0.00340.0185-1.9834-24.01431.557
21.0081-0.07730.13370.60930.14270.5239-0.00020.0819-0.03310.01720.0009-0.01260.00730.0037-0.00070.0051-0.0065-0.00450.01650.0030.005329.5836-66.81560.078
30.60840.15110.04220.6981-0.16880.7430.00950.00770.03690.05350.0077-0.0198-0.00630.0222-0.01730.02870.00310.00440.0048-0.0120.0444-14.9296-77.6013-1.7341
40.51840.10830.03680.8059-0.18280.8123-0.0023-0.02050.0740.07460.0152-0.0648-0.06210.0719-0.01290.05040.0136-0.00740.0229-0.03130.086932.5062-18.073456.6735
500000000000000-00.1276000.127600.1276000
Refinement TLS groupSelection: ALL

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