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- PDB-2c6n: Structure of human somatic angiontensin-I converting enzyme N dom... -

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Entry
Database: PDB / ID: 2c6n
TitleStructure of human somatic angiontensin-I converting enzyme N domain with lisinopril
ComponentsANGIOTENSIN-CONVERTING ENZYME, SOMATIC ISOFORM
KeywordsHYDROLASE/HYDROLASE INHIBITOR / HYDROLASE / ANGIOTENSIN-I CONVERTING ENZYME / N DOMAIN / ZINC METALLOPEPTIDASE / METALLOPROTEASE / ANGIOTENSIN / LISINOPRIL / CARBOXYPEPTIDASE / GLYCOPROTEIN / METAL-BINDING / PHOSPHORYLATION / PROTEASE / TRANSMEMBRANE / HYDROLASE-HYDROLASE INHIBITOR COMPLEX
Function / homology
Function and homology information


: / positive regulation of peptidyl-tyrosine autophosphorylation / 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 ...: / positive regulation of peptidyl-tyrosine autophosphorylation / 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 / positive regulation of blood pressure / negative regulation of glucose import / vasoconstriction / neutrophil mediated immunity / hormone metabolic process / Hydrolases; Glycosylases; Glycosidases, i.e. enzymes that hydrolyse O- and S-glycosyl compounds / 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 / arachidonic acid secretion / post-transcriptional regulation of gene expression / eating behavior / 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 / positive regulation of protein tyrosine kinase activity / 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 / negative regulation of protein binding / 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 / positive regulation of protein binding / peptidase activity / spermatogenesis / endopeptidase activity / response to lipopolysaccharide / lysosome / membrane => GO:0016020 / 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
Lisinopril / ACETATE ION / Chem-LPR / Angiotensin-converting enzyme / Angiotensin-converting enzyme
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsCorradi, H.R. / Schwager, S.L.U. / Nichinda, A. / Sturrock, E.D. / Acharya, K.R.
CitationJournal: J. Mol. Biol. / Year: 2006
Title: Crystal structure of the N domain of human somatic angiotensin I-converting enzyme provides a structural basis for domain-specific inhibitor design.
Authors: Corradi, H.R. / Schwager, S.L. / Nchinda, A.T. / Sturrock, E.D. / Acharya, K.R.
History
DepositionNov 10, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 15, 2006Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Non-polymer description / Structure summary / Version format compliance
Revision 1.2Mar 6, 2013Group: Other
Revision 1.3Apr 15, 2015Group: Data collection / Database references / Source and taxonomy
Revision 2.0Jul 25, 2018Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Refinement description / Source and taxonomy / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / citation / citation_author / database_PDB_caveat / entity / entity_src_gen / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_chiral / refine / struct_asym / struct_conn
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_atom_id / _atom_site.auth_comp_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _citation.journal_abbrev / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation_author.name / _entity_src_gen.host_org_common_name / _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _pdbx_nonpoly_scheme.entity_id / _pdbx_nonpoly_scheme.mon_id / _pdbx_nonpoly_scheme.pdb_mon_id / _refine.pdbx_starting_model / _struct_asym.entity_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id
Revision 2.1Jul 1, 2020Group: Advisory / Data collection ...Advisory / Data collection / Derived calculations / Other
Category: chem_comp / pdbx_database_status ...chem_comp / pdbx_database_status / pdbx_struct_conn_angle / pdbx_validate_close_contact / struct_conn
Item: _chem_comp.type / _pdbx_database_status.status_code_sf ..._chem_comp.type / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value
Revision 3.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_PDB_caveat / 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_molecule / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / pdbx_validate_chiral / pdbx_validate_close_contact / 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 / _chem_comp.name / _database_PDB_caveat.text / _pdbx_entity_nonpoly.entity_id / _pdbx_entity_nonpoly.name / _pdbx_molecule.asym_id / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_validate_chiral.auth_asym_id / _pdbx_validate_chiral.auth_seq_id / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_2 / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 3.1Dec 13, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ANGIOTENSIN-CONVERTING ENZYME, SOMATIC ISOFORM
B: ANGIOTENSIN-CONVERTING ENZYME, SOMATIC ISOFORM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)144,06217
Polymers141,0722
Non-polymers2,99015
Water34219
1
A: ANGIOTENSIN-CONVERTING ENZYME, SOMATIC ISOFORM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,0949
Polymers70,5361
Non-polymers1,5578
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: ANGIOTENSIN-CONVERTING ENZYME, SOMATIC ISOFORM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,9688
Polymers70,5361
Non-polymers1,4327
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)101.300, 210.900, 171.000
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein ANGIOTENSIN-CONVERTING ENZYME, SOMATIC ISOFORM / / SOMATIC ANGIOTENSIN-I CONVERTING ENZYME N DOMAIN / DIPEPTIDYL CARBOXYPEPTIDASE I / KININASE II / CD143 ANTIGEN


Mass: 70536.148 Da / Num. of mol.: 2 / Fragment: N DOMAIN, RESIDUES 38-649
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Cell line (production host): CHO-K1 / Production host: Cricetulus griseus (Chinese hamster)
References: UniProt: Q59GY8, UniProt: P12821*PLUS, peptidyl-dipeptidase A

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Sugars , 2 types, 6 molecules

#2: 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: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam 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
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#3: 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.: 4
Source method: isolated from a genetically manipulated source
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

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Non-polymers , 6 types, 28 molecules

#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#5: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-LPR / [N2-[(S)-1-CARBOXY-3-PHENYLPROPYL]-L-LYSYL-L-PROLINE / / LISINOPRIL / Lisinopril


Type: Oligopeptide / Class: Enzyme inhibitor / Mass: 405.488 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H31N3O5 / References: Lisinopril / Comment: medication, inhibitor*YM
#7: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#8: Chemical ChemComp-ACT / ACETATE ION / Acetate


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


Mass: 18.015 Da / Num. of mol.: 19 / Source method: isolated from a natural source / Formula: H2O

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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: 3.39 Å3/Da / Density % sol: 63.44 %
Crystal growpH: 4.9
Details: 0.2M LITHIUM SULPHATE, 0.1M SODIUM ACETATE, PH 4.9, 10UM ZINC SULPHATE, 18% POLYETHYLENE GLYCOL 4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX14.1 / Wavelength: 1.488
DetectorType: ADSC CCD / Detector: CCD / Date: May 19, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.488 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. obs: 36858 / % possible obs: 95.5 % / Observed criterion σ(I): 2 / Redundancy: 4 % / Biso Wilson estimate: 50.2 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 10.2
Reflection shellResolution: 3→3.16 Å / Rmerge(I) obs: 0.35 / Mean I/σ(I) obs: 2.2 / % possible all: 85.3

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Processing

Software
NameVersionClassification
CNS1.1refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1O8A

1o8a


Resolution: 3→28.76 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 2443102.53 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.308 903 2.6 %RANDOM
Rwork0.294 ---
obs0.294 35238 95.1 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 39.17 Å2 / ksol: 0.35 e/Å3
Displacement parametersBiso mean: 38.2 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.54 Å0.5 Å
Luzzati d res low-5 Å
Luzzati sigma a0.5 Å0.61 Å
Refinement stepCycle: LAST / Resolution: 3→28.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9412 0 190 19 9621
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.014
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg2.2
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.8
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.95
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 3→3.19 Å / Rfactor Rfree error: 0.031 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.356 130 2.5 %
Rwork0.375 5119 -
obs--86.1 %
Xplor fileSerial no: 1 / Param file: PROTEIN_REP.PARAM / Topol file: PROTEIN.TOP

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