[English] 日本語
Yorodumi
- PDB-7z70: Crystal structure of Angiotensin-1 converting enzyme C-domain in ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7z70
TitleCrystal structure of Angiotensin-1 converting enzyme C-domain in complex with fosinoprilat
ComponentsAngiotensin-converting enzyme
KeywordsHYDROLASE / Angiotensin-1 converting enzyme / fosinoprilat / fosinopril / Metalloprotease
Function / homology
Function and homology information


mononuclear cell proliferation / cell proliferation in bone marrow / tripeptidyl-peptidase activity / bradykinin receptor binding / regulation of angiotensin metabolic process / exopeptidase activity / substance P catabolic process / response to laminar fluid shear stress / peptidyl-dipeptidase A / regulation of renal output by angiotensin ...mononuclear cell proliferation / cell proliferation in bone marrow / tripeptidyl-peptidase activity / bradykinin receptor binding / regulation of angiotensin metabolic process / exopeptidase activity / substance P catabolic process / response to laminar fluid shear stress / peptidyl-dipeptidase A / regulation of renal output by angiotensin / negative regulation of calcium ion import / positive regulation of peptidyl-cysteine S-nitrosylation / positive regulation of systemic arterial blood pressure / negative regulation of gap junction assembly / metallodipeptidase activity / cellular response to aldosterone / hormone catabolic process / bradykinin catabolic process / angiogenesis involved in coronary vascular morphogenesis / response to thyroid hormone / negative regulation of glucose import / vasoconstriction / neutrophil mediated immunity / hormone metabolic process / regulation of hematopoietic stem cell proliferation / regulation of smooth muscle cell migration / antigen processing and presentation of peptide antigen via MHC class I / mitogen-activated protein kinase binding / embryo development ending in birth or egg hatching / positive regulation of neurogenesis / chloride ion binding / mitogen-activated protein kinase kinase binding / eating behavior / arachidonic acid secretion / post-transcriptional regulation of gene expression / lung alveolus development / peptide catabolic process / heterocyclic compound binding / heart contraction / 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 / angiotensin maturation / hematopoietic stem cell differentiation / blood vessel remodeling / Metabolism of Angiotensinogen to Angiotensins / animal organ regeneration / amyloid-beta metabolic process / carboxypeptidase activity / positive regulation of vasoconstriction / sperm midpiece / blood vessel diameter maintenance / response to nutrient levels / basal plasma membrane / kidney development / female pregnancy / angiotensin-activated signaling pathway / cellular response to glucose stimulus / brush border membrane / regulation of synaptic plasticity / metalloendopeptidase activity / regulation of blood pressure / male gonad development / metallopeptidase activity / actin binding / peptidase activity / spermatogenesis / endopeptidase activity / response to lipopolysaccharide / lysosome / response to hypoxia / calmodulin binding / endosome / response to xenobiotic stimulus / positive regulation of apoptotic process / external side of plasma membrane / negative regulation of gene expression / proteolysis / extracellular space / extracellular exosome / zinc ion binding / 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 / BORIC ACID / IMIDAZOLE / fosinoprilat / Angiotensin-converting enzyme
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsCozier, G.E. / Acharya, K.R.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom)MR/M026647/1 United Kingdom
CitationJournal: Febs J. / Year: 2022
Title: Structural basis for the inhibition of human angiotensin-1 converting enzyme by fosinoprilat.
Authors: Cozier, G.E. / Newby, E.C. / Schwager, S.L.U. / Isaac, R.E. / Sturrock, E.D. / Acharya, K.R.
History
DepositionMar 14, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 22, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 16, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Angiotensin-converting enzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,00414
Polymers68,8781
Non-polymers2,12613
Water10,665592
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)56.563, 85.987, 134.686
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

-
Components

-
Protein , 1 types, 1 molecules A

#1: Protein Angiotensin-converting enzyme / / ACE / Dipeptidyl carboxypeptidase I / Kininase II


Mass: 68877.875 Da / Num. of mol.: 1 / Mutation: E64G, N90Q, N155Q, N337Q, N586Q
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, Hydrolases; Glycosylases; Glycosidases, i.e. enzymes that hydrolyse O- and S-glycosyl compounds, peptidyl-dipeptidase A

-
Sugars , 2 types, 2 molecules

#2: Polysaccharide alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 894.823 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3DManpb1-4DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/4,5,4/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5][a1221m-1a_1-5]/1-1-2-3-4/a4-b1_a6-e1_b4-c1_c3-d1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}}}[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
#4: 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 / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1 / 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

-
Non-polymers , 8 types, 603 molecules

#3: Chemical ChemComp-KS8 / fosinoprilat / Fosinopril


Mass: 435.494 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H34NO5P / Feature type: SUBJECT OF INVESTIGATION / Comment: inhibitor*YM
#5: Chemical ChemComp-BO3 / BORIC ACID / Boric acid


Mass: 61.833 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: BH3O3
#6: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#7: Chemical ChemComp-IMD / IMIDAZOLE / Imidazole


Mass: 69.085 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H5N2
#8: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#9: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#10: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#11: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 592 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.38 Å3/Da / Density % sol: 48.27 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 4 / Details: 0.1 M MIB pH 4.0, 5% glycerol, 15% PEG 3350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Feb 5, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.85→134.69 Å / Num. obs: 56970 / % possible obs: 100 % / Redundancy: 13 % / Biso Wilson estimate: 21.83 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.341 / Rpim(I) all: 0.098 / Net I/σ(I): 5.2
Reflection shellResolution: 1.85→1.89 Å / Mean I/σ(I) obs: 0.7 / Num. unique obs: 3456 / CC1/2: 0.327

-
Processing

Software
NameVersionClassification
PHENIX1.19.1_4122refinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6F9T

6f9t


Resolution: 1.85→52.15 Å / SU ML: 0.2418 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.3981
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2134 2017 3.57 %
Rwork0.1736 54491 -
obs0.175 56508 99.32 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 26.35 Å2
Refinement stepCycle: LAST / Resolution: 1.85→52.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4690 0 136 592 5418
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00545009
X-RAY DIFFRACTIONf_angle_d0.76806
X-RAY DIFFRACTIONf_chiral_restr0.043728
X-RAY DIFFRACTIONf_plane_restr0.0063871
X-RAY DIFFRACTIONf_dihedral_angle_d14.90281856
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.85-1.90.36031450.31593813X-RAY DIFFRACTION98.78
1.9-1.950.28771640.27723822X-RAY DIFFRACTION98.91
1.95-20.31881400.263793X-RAY DIFFRACTION98.97
2-2.070.26011260.22333852X-RAY DIFFRACTION99
2.07-2.140.23891230.2073861X-RAY DIFFRACTION99.03
2.14-2.230.26041460.18913823X-RAY DIFFRACTION99.15
2.23-2.330.21891420.18213882X-RAY DIFFRACTION99.09
2.33-2.450.20981520.16153869X-RAY DIFFRACTION99.28
2.45-2.610.2021470.15813852X-RAY DIFFRACTION99.58
2.61-2.810.20741390.15993905X-RAY DIFFRACTION99.63
2.81-3.090.21451450.15713924X-RAY DIFFRACTION99.78
3.09-3.540.19831420.15223954X-RAY DIFFRACTION99.71
3.54-4.460.17741430.14023994X-RAY DIFFRACTION99.9
4.46-52.150.17561630.16254147X-RAY DIFFRACTION99.68
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)
11.32563985595-0.864063989548-0.5636285166016.419475017323.328330579253.030672833970.0486762500060.143824471704-0.1154730886450.000252168457645-0.2706669260180.05769977122210.239198849427-0.1483695093420.1801942733990.215152592102-0.02684873657920.005669267870980.288083908115-0.01198107685090.15810541070411.0849885895-6.898617569261.17408775117
22.232744513561.51242740045-0.139749902281.772915914460.7612050601051.67991656352-0.1696010316950.136232501863-0.103430845581-0.3267042150170.01937076407870.3449109728530.204280915521-0.02683260854930.1276405982950.235699328143-0.0048001878794-0.006366563452650.257695205795-0.001118434800090.1248999351763.63465797901-7.594573557294.63594092672
30.6080211412650.3010784854590.1735972138212.140429629450.59788143090.948019659498-0.006599107069090.04773644645370.11152038479-0.232045873539-0.01736353664480.0719290087302-0.17045880253-0.06140810276250.04637854399010.142895836920.006169576711750.004440725422980.1756617782240.01869562836370.1518700456280.67220712155412.078742889320.6695368483
40.541982848184-0.6945410891190.3297728604683.656984125922.469508591383.400374271370.0291286537127-0.0261514665005-0.03165227781980.594980231639-0.0206627381399-0.112945891380.346188860056-0.0175334182047-0.005414411190870.124465664901-0.0007799564277280.01049833055720.1790485405520.007217110055970.13998468357810.03317577365.5580399480842.9700359727
51.00434575932-0.313874558350.05582076997461.226375636470.5020316309841.952142745672.53483129256E-5-0.002107983042260.1021737512270.00554073483380.119457808698-0.170455738925-0.2011180948480.223644918601-0.08702635269640.17176366065-0.0116650528274-0.007933945903080.164983644013-0.0210587421860.17527344303613.963628151918.584701394440.8433441016
61.75107990767-0.2634352430250.3966694745082.175271480420.2905037309981.73232254839-0.02817233926660.1022659565780.141689177669-0.1470505534780.0538001948938-0.172832223737-0.141256313610.211995873299-0.01960656775040.155675392166-0.04332055648170.0328950851740.1790249071210.009770358209360.16032430135623.912750156410.723898592315.2217094742
71.15778277271-0.193666162379-0.294437548121.41927195268-0.08419543726331.08201699411-0.054180787241-0.07224509607060.1553182952550.02913271410490.0767204810835-0.245561761136-0.07329666122510.205702349477-0.0274123508710.07416776908680.013188739904-0.00413461039940.16394688113-0.01171287336830.18832156754725.10097695444.6565586805328.7405098286
8-0.00140059400729-0.00410806824050.03991333035131.037020007880.1521134393340.822877222704-0.01908141431590.03770329355260.03590633717090.028391255407-0.02000725362040.08252687212270.0039241244427-0.08311926021320.04377805295160.126071853624-0.0121974647202-0.004761723131560.1584956874050.001676455694610.1479804333573.733213166095.0275209695630.2699422001
92.502900388120.587335201702-0.05496218361730.6863720292060.4515054384450.827790341595-0.130472139322-0.119950823943-0.11933749890.1100404082270.136900788699-0.1673909747550.1756130014620.346574524925-0.04356539464450.1473456288470.0528040915667-0.01352993160130.247864838256-0.03612159963020.2596758402332.3896166339-4.1943176018327.9220653802
100.614369142216-0.558406540296-0.3899298521262.157372171372.075164963.65387695969-0.0735404947321-0.0591895650066-0.01259218597820.3019579068480.179036067865-0.19306280940.2165310479510.259567418381-0.08256711508580.158111399643-0.00471241232942-0.02507516852220.1413093494110.02970819985820.15485303962417.6842897975-2.5751190288439.7997072336
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid 40 through 70 )40 - 701 - 31
22chain 'A' and (resid 71 through 128 )71 - 12832 - 89
33chain 'A' and (resid 129 through 228 )129 - 22890 - 189
44chain 'A' and (resid 229 through 259 )229 - 259190 - 220
55chain 'A' and (resid 260 through 300 )260 - 300221 - 261
66chain 'A' and (resid 301 through 393 )301 - 393262 - 354
77chain 'A' and (resid 394 through 455 )394 - 455355 - 413
88chain 'A' and (resid 456 through 540 )456 - 540414 - 498
99chain 'A' and (resid 541 through 568 )541 - 568499 - 526
1010chain 'A' and (resid 569 through 617 )569 - 617527 - 575

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more