[English] 日本語
Yorodumi
- PDB-9qaq: Human angiotensin-1 converting enzyme C-domain in complex with pe... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9qaq
TitleHuman angiotensin-1 converting enzyme C-domain in complex with perindoprilat
ComponentsAngiotensin-converting enzyme, soluble form
KeywordsHYDROLASE / inhibitor / complex / perindopril
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 / antigen processing and presentation of peptide antigen via MHC class I / positive regulation of systemic arterial blood pressure / 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
IMIDAZOLE / PERINDOPRILAT / Angiotensin-converting enzyme
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 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: Febs J. / Year: 2025
Title: Molecular basis of domain-specific angiotensin I-converting enzyme inhibition by the antihypertensive drugs enalaprilat, ramiprilat, trandolaprilat, quinaprilat and perindoprilat.
Authors: Gregory, K.S. / Ramasamy, V. / Sturrock, E.D. / Acharya, K.R.
History
DepositionFeb 28, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 3, 2025Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Angiotensin-converting enzyme, soluble form
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,87215
Polymers66,7791
Non-polymers2,09314
Water5,332296
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3350 Å2
ΔGint13 kcal/mol
Surface area23490 Å2
Unit cell
Length a, b, c (Å)56.484, 85.119, 133.829
Angle α, β, γ (deg.)90, 90, 90
Int Tables number19
Space group name H-MP212121

-
Components

-
Protein , 1 types, 1 molecules A

#1: Protein Angiotensin-converting enzyme, soluble form


Mass: 66778.547 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

-
Sugars , 2 types, 3 molecules

#2: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1- ...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: 732.682 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1221m-1a_1-5]/1-1-2-3/a4-b1_a6-d1_b4-c1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}[(6+1)][a-L-Fucp]{}}LINUCSPDB-CARE
#8: 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: isolated from a natural source / Formula: C8H15NO6 / Feature type: SUBJECT OF INVESTIGATION
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 , 6 types, 307 molecules

#3: Chemical ChemComp-ZN / ZINC ION


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


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


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


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#7: Chemical ChemComp-X94 / PERINDOPRILAT


Mass: 340.415 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H28N2O5
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 296 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.42 Å3/Da / Density % sol: 49.15 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, hanging drop / pH: 4 / Details: 0.1 M MIB pH 4, 5% glycerol, 15% PEG 3350

-
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: Jul 1, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.953731 Å / Relative weight: 1
ReflectionResolution: 1.9→133.83 Å / Num. obs: 51757 / % possible obs: 100 % / Redundancy: 13.2 % / CC1/2: 0.997 / Rpim(I) all: 0.066 / Net I/σ(I): 8.3
Reflection shellResolution: 1.9→1.94 Å / Num. unique obs: 3296 / CC1/2: 0.45 / Rpim(I) all: 0.792

-
Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→71.926 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.934 / WRfactor Rfree: 0.201 / WRfactor Rwork: 0.152 / Average fsc free: 0.9583 / Average fsc work: 0.973 / Cross valid method: FREE R-VALUE / ESU R: 0.138 / ESU R Free: 0.139
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2221 2545 4.925 %
Rwork0.1686 49126 -
all0.171 --
obs-51671 99.975 %
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: 31.602 Å2
Baniso -1Baniso -2Baniso -3
1-1.663 Å20 Å20 Å2
2---0.542 Å20 Å2
3----1.12 Å2
Refinement stepCycle: LAST / Resolution: 1.9→71.926 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4689 0 133 296 5118
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0124961
X-RAY DIFFRACTIONr_bond_other_d00.0164534
X-RAY DIFFRACTIONr_angle_refined_deg2.3321.8326734
X-RAY DIFFRACTIONr_angle_other_deg0.7511.75810473
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2615572
X-RAY DIFFRACTIONr_dihedral_angle_2_deg7.481527
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.23610803
X-RAY DIFFRACTIONr_dihedral_angle_6_deg15.60910242
X-RAY DIFFRACTIONr_chiral_restr0.1140.2721
X-RAY DIFFRACTIONr_chiral_restr_other00.21
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.025792
X-RAY DIFFRACTIONr_gen_planes_other0.030.021170
X-RAY DIFFRACTIONr_nbd_refined0.2440.21109
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2110.24222
X-RAY DIFFRACTIONr_nbtor_refined0.1950.22461
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0880.22582
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1550.2256
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0710.22
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.270.211
X-RAY DIFFRACTIONr_nbd_other0.2170.240
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2390.212
X-RAY DIFFRACTIONr_mcbond_it3.4192.8212300
X-RAY DIFFRACTIONr_mcbond_other3.4192.8212300
X-RAY DIFFRACTIONr_mcangle_it4.2785.0492868
X-RAY DIFFRACTIONr_mcangle_other4.2775.0492869
X-RAY DIFFRACTIONr_scbond_it5.3023.362661
X-RAY DIFFRACTIONr_scbond_other5.3013.3612662
X-RAY DIFFRACTIONr_scangle_it7.5015.9163866
X-RAY DIFFRACTIONr_scangle_other7.55.9163867
X-RAY DIFFRACTIONr_lrange_it8.45229.0935790
X-RAY DIFFRACTIONr_lrange_other8.45229.0955791
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
1.9-1.9490.2871690.30136150.30137840.9170.9271000.303
1.949-2.0030.3181930.27434850.27736790.9250.9499.97280.274
2.003-2.0610.2881730.23133620.23435380.9390.95999.91520.227
2.061-2.1240.2591730.21632950.21834720.9530.96799.88480.209
2.124-2.1940.2681720.20532130.20833850.9540.9711000.193
2.194-2.2710.2531820.19830960.20132780.9570.9741000.185
2.271-2.3560.2331740.17329740.17731490.9630.9899.96820.158
2.356-2.4520.2321420.16128850.16530270.970.9841000.146
2.452-2.5610.2011270.15728060.15929340.9760.98599.96590.14
2.561-2.6860.2551350.16326570.16727920.9560.9841000.145
2.686-2.8310.2521260.16225460.16726740.9650.98499.92520.144
2.831-3.0030.2411140.15324110.15625250.9670.9861000.137
3.003-3.210.2191300.16122360.16423660.9720.9841000.148
3.21-3.4660.2231130.16921100.17122230.9710.9831000.158
3.466-3.7960.209960.15819820.16120780.9750.9871000.15
3.796-4.2430.162930.13117710.13318640.9860.991000.125
4.243-4.8960.147810.11415850.11616660.9890.9931000.109
4.896-5.990.223710.14613650.1514360.9750.991000.139
5.99-8.4410.174500.15910820.15911320.9780.9861000.152
8.441-71.9260.224310.1756500.1786820.9690.97299.85340.174

+
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