[English] 日本語
Yorodumi
- PDB-4apj: Human angiotensin-converting enzyme in complex with BPPb -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4apj
TitleHuman angiotensin-converting enzyme in complex with BPPb
Components
  • ANGIOTENSIN-CONVERTING ENZYME
  • BRADYKININ-POTENTIATING PEPTIDE B
KeywordsHYDROLASE/HORMONE / HYDROLASE-HORMONE COMPLEX / ZINC METALLOPROTEASE / METALLOPEPTIDASE
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 / metalloendopeptidase inhibitor activity / tripeptidyl-peptidase activity / regulation of renal output by angiotensin ...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 / metalloendopeptidase inhibitor activity / 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 / eating behavior / post-transcriptional regulation of gene expression / 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 / hematopoietic stem cell differentiation / peptidyl-dipeptidase activity / blood vessel remodeling / amyloid-beta metabolic process / angiotensin maturation / animal organ regeneration / Metabolism of Angiotensinogen to Angiotensins / positive regulation of vasoconstriction / carboxypeptidase activity / 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 / hormone activity / metalloendopeptidase activity / regulation of blood pressure / vasodilation / metallopeptidase activity / male gonad development / peptidase activity / actin binding / toxin activity / 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
Natriuretic peptide, conserved site / Atrial natriuretic peptide / Natriuretic peptides signature. / Natriuretic peptide / Natriuretic peptide / 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 / Bradykinin-potentiating and C-type natriuretic peptides / Angiotensin-converting enzyme
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
GLOYDIUS BLOMHOFFI (mamushi)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsMasuyer, G. / Schwager, S.L.U. / Sturrock, E.D. / Isaac, R.E. / Acharya, K.R.
CitationJournal: Sci.Rep. / Year: 2012
Title: Molecular Recognition and Regulation of Human Angiotensin-I Converting Enzyme (Ace) Activity by Natural Inhibitory Peptides.
Authors: Masuyer, G. / Schwager, S.L.U. / Sturrock, E.D. / Isaac, R.E. / Acharya, K.R.
History
DepositionApr 3, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 17, 2012Provider: repository / Type: Initial release
Revision 1.1Oct 24, 2012Group: Database references
Revision 2.0Mar 11, 2020Group: Data collection / Derived calculations ...Data collection / Derived calculations / Other / Polymer sequence
Category: chem_comp / entity_poly ...chem_comp / entity_poly / pdbx_database_status / struct_conn
Item: _chem_comp.type / _entity_poly.pdbx_seq_one_letter_code_can ..._chem_comp.type / _entity_poly.pdbx_seq_one_letter_code_can / _pdbx_database_status.status_code_sf / _struct_conn.pdbx_leaving_atom_flag
Revision 3.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_unobs_or_zero_occ_atoms / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _atom_site_anisotrop.pdbx_label_asym_id / _chem_comp.name / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_unobs_or_zero_occ_atoms.label_asym_id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 3.1Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: ANGIOTENSIN-CONVERTING ENZYME
P: BRADYKININ-POTENTIATING PEPTIDE B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,16511
Polymers69,2532
Non-polymers1,9119
Water2,234124
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4710 Å2
ΔGint-36 kcal/mol
Surface area25280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.870, 85.280, 133.220
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

-
Protein / Protein/peptide / Sugars , 3 types, 3 molecules AP

#1: Protein ANGIOTENSIN-CONVERTING ENZYME / ACE / DIPEPTIDYL CARBOXYPEPTIDASE I / KININASE II / CD143 / ACE-T


Mass: 68068.922 Da / Num. of mol.: 1 / Fragment: EXTRACELLULAR DOMAIN, RESIDUES 68-656
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / 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
#2: Protein/peptide BRADYKININ-POTENTIATING PEPTIDE B / POTENTIATOR B


Mass: 1184.429 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) GLOYDIUS BLOMHOFFI (mamushi) / References: UniProt: P01021
#3: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}}LINUCSPDB-CARE

-
Non-polymers , 5 types, 132 molecules

#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#6: Chemical ChemComp-PE4 / 2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL / POLYETHYLENE GLYCOL PEG4000


Mass: 354.436 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C16H34O8 / Comment: precipitant*YM
#7: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 124 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.4 Å3/Da / Density % sol: 49 % / Description: NONE
Crystal growpH: 4.7
Details: 50MM SODIUM ACETATE PH 4.7, 15% PEG4000, 10UM ZNSO4

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.979
DetectorType: DECTRIS PILATUS-2M / Detector: PIXEL / Date: Feb 9, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.6→71.82 Å / Num. obs: 20038 / % possible obs: 97.7 % / Observed criterion σ(I): 0 / Redundancy: 4.8 % / Rmerge(I) obs: 0.13 / Net I/σ(I): 10.4
Reflection shellResolution: 2.6→2.74 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.48 / Mean I/σ(I) obs: 3.5 / % possible all: 97.2

-
Processing

Software
NameVersionClassification
REFMAC5.5.0109refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1O8A

1o8a


Resolution: 2.6→71.82 Å / Cor.coef. Fo:Fc: 0.908 / Cor.coef. Fo:Fc free: 0.868 / SU B: 24.515 / SU ML: 0.248 / Cross valid method: THROUGHOUT / ESU R Free: 0.354 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.25611 1028 5.1 %RANDOM
Rwork0.21518 ---
obs0.21723 18936 96.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.597 Å2
Baniso -1Baniso -2Baniso -3
1--0.67 Å20 Å20 Å2
2---0.16 Å20 Å2
3---0.84 Å2
Refinement stepCycle: LAST / Resolution: 2.6→71.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4833 0 99 124 5056
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0225085
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg0.9761.9596905
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.8235591
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.84124.24250
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.49415823
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.1521527
X-RAY DIFFRACTIONr_chiral_restr0.0660.2724
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0213899
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.2681.52976
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.5224809
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.63232109
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it1.1364.52096
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.6→2.667 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.318 93 -
Rwork0.237 1345 -
obs--96.32 %
Refinement TLS params.Method: refined / Origin x: 12.3897 Å / Origin y: -6.0983 Å / Origin z: -23.4708 Å
111213212223313233
T0.0109 Å20.0039 Å20.0013 Å2-0.0202 Å20.0144 Å2--0.0342 Å2
L0.222 °2-0.1141 °2-0.0396 °2-0.661 °20.4899 °2--0.6691 °2
S-0.0083 Å °-0.0053 Å °-0.0131 Å °0.0539 Å °0.0411 Å °-0.0647 Å °0.0351 Å °0.0351 Å °-0.0327 Å °

+
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://pdbjlvh1.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