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- PDB-2oc2: Structure of testis ACE with RXPA380 -

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Basic information

Entry
Database: PDB / ID: 2oc2
TitleStructure of testis ACE with RXPA380
ComponentsAngiotensin-converting enzyme, somatic isoform
KeywordsHYDROLASE / enzyme-inhibitor complex
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
Chem-RX3 / Angiotensin-converting enzyme
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / phases known / Resolution: 2.25 Å
AuthorsCorradi, H.R. / Anthony, C.S. / Schwager, S.L. / Redelinghuys, P. / Georgiadis, D. / Dive, V. / Acharya, K.R. / Sturrock, E.D.
Citation
Journal: Biochemistry / Year: 2007
Title: The structure of testis angiotensin-converting enzyme in complex with the C domain-specific inhibitor RXPA380.
Authors: Corradi, H.R. / Chitapi, I. / Sewell, B.T. / Georgiadis, D. / Dive, V. / Sturrock, E.D. / Acharya, K.R.
#1: Journal: J.Biol.Chem. / Year: 2010
Title: The N domain of human angiotensin-I converting enzyme: the role of N-glycosylation and the crystal structure in complex with an N domain specific phosphinic inhibitor RXP407.
Authors: Anthony, C.S. / Corradi, H.R. / Schwager, S.L. / Redelinghuys, P. / Georgiadis, D. / Dive, V. / Acharya, K.R. / Sturrock, E.D.
History
DepositionDec 20, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 22, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 11, 2012Group: Non-polymer description
Revision 1.4Dec 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / entity / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _chem_comp.name / _database_2.pdbx_DOI ..._chem_comp.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _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 / _struct_conn.pdbx_dist_value / _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_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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Mar 20, 2024Group: Database references / Category: citation / citation_author
Revision 1.6Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Angiotensin-converting enzyme, somatic isoform
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,0515
Polymers68,2971
Non-polymers7544
Water1,928107
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)56.514, 84.763, 133.483
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Angiotensin-converting enzyme, somatic isoform / / E.C.3.4.15.1 / Dipeptidyl carboxypeptidase I / Kininase II / CD143 antigen


Mass: 68297.195 Da / Num. of mol.: 1 / Fragment: Peptidase M2 2 (residues 631-1232)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ACE, DCP, DCP1 / Plasmid: pEE-ACEDelta36NJ / Cell (production host): Hampster Ovary cells / Production host: Cricetulus griseus (Chinese hamster) / Strain (production host): CHO-K1 / References: UniProt: P12821, peptidyl-dipeptidase A
#2: Chemical ChemComp-ZN / ZINC ION


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


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-RX3 / N-({(1S,2R)-2-[(S)-[(1R)-1-{[(BENZYLOXY)CARBONYL]AMINO}-2-PHENYLETHYL](HYDROXY)PHOSPHORYL]CYCLOPENTYL}CARBONYL)-L-TRYPT OPHAN / RXPA380


Mass: 617.629 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C33H36N3O7P
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 107 / 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: 2.34 Å3/Da / Density % sol: 47.42 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 4.7
Details: 13.5% PEG 4000, 0.12M Na Malonate, 90mM Na Acetate pH 4.7, 9uM Zn Acetate , VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X13 / Wavelength: 0.8073 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: May 15, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8073 Å / Relative weight: 1
ReflectionResolution: 2.25→20 Å / Num. all: 22494 / Num. obs: 22494 / % possible obs: 72.2 % / Observed criterion σ(I): 0 / Biso Wilson estimate: 31.3 Å2 / Rsym value: 0.103 / Net I/σ(I): 7.1
Reflection shellResolution: 2.25→2.33 Å / Mean I/σ(I) obs: 1.53 / Rsym value: 0.461 / % possible all: 59.1

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0005refinement
PDB_EXTRACT2data extraction
HKL-2000data collection
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: phases known
Starting model: testis ACE

Resolution: 2.25→17.12 Å / Cor.coef. Fo:Fc: 0.916 / Cor.coef. Fo:Fc free: 0.879 / SU B: 7.76 / SU ML: 0.195 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.842 / ESU R Free: 0.317 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.262 926 4.1 %RANDOM
Rwork0.215 ---
all0.217 22492 --
obs0.217 22492 72.32 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.05 Å2
Baniso -1Baniso -2Baniso -3
1--0.04 Å20 Å20 Å2
2--0.04 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.25→17.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4751 0 47 107 4905
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0224920
X-RAY DIFFRACTIONr_angle_refined_deg1.2071.9476701
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3445583
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.01224.132242
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.97215789
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.9261526
X-RAY DIFFRACTIONr_chiral_restr0.0780.2699
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.023833
X-RAY DIFFRACTIONr_nbd_refined0.1880.22465
X-RAY DIFFRACTIONr_nbtor_refined0.2970.23344
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1370.2212
X-RAY DIFFRACTIONr_metal_ion_refined0.0710.24
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.210.251
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1590.24
X-RAY DIFFRACTIONr_mcbond_it0.4031.52999
X-RAY DIFFRACTIONr_mcangle_it0.69524703
X-RAY DIFFRACTIONr_scbond_it0.90732253
X-RAY DIFFRACTIONr_scangle_it1.3924.51997
LS refinement shellResolution: 2.25→2.307 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.419 43 -
Rwork0.319 1258 -
obs-1301 58.79 %

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