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- PDB-2oi0: Crystal structure analysis 0f the TNF-a Coverting Enzyme (TACE) i... -

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Basic information

Entry
Database: PDB / ID: 2oi0
TitleCrystal structure analysis 0f the TNF-a Coverting Enzyme (TACE) in complexed with Aryl-sulfonamide
ComponentsTNF- a Converting Enzyme (TACE)
KeywordsHYDROLASE / TNF-a Coverting enzyme / Aryl-sulfonamide / TACE inhibitors
Function / homology
Function and homology information


ADAM 17 endopeptidase / regulation of mast cell apoptotic process / metalloendopeptidase activity involved in amyloid precursor protein catabolic process / cellular response to high density lipoprotein particle stimulus / positive regulation of epidermal growth factor-activated receptor activity / Constitutive Signaling by NOTCH1 t(7;9)(NOTCH1:M1580_K2555) Translocation Mutant / Notch receptor processing / interleukin-6 receptor binding / tumor necrosis factor binding / positive regulation of T cell chemotaxis ...ADAM 17 endopeptidase / regulation of mast cell apoptotic process / metalloendopeptidase activity involved in amyloid precursor protein catabolic process / cellular response to high density lipoprotein particle stimulus / positive regulation of epidermal growth factor-activated receptor activity / Constitutive Signaling by NOTCH1 t(7;9)(NOTCH1:M1580_K2555) Translocation Mutant / Notch receptor processing / interleukin-6 receptor binding / tumor necrosis factor binding / positive regulation of T cell chemotaxis / TNF signaling / positive regulation of leukocyte chemotaxis / germinal center formation / Regulated proteolysis of p75NTR / Release of Hh-Np from the secreting cell / commissural neuron axon guidance / positive regulation of tumor necrosis factor-mediated signaling pathway / neutrophil mediated immunity / Notch binding / wound healing, spreading of epidermal cells / negative regulation of cold-induced thermogenesis / CD163 mediating an anti-inflammatory response / positive regulation of vascular endothelial cell proliferation / cell adhesion mediated by integrin / positive regulation of epidermal growth factor receptor signaling pathway / Signaling by EGFR / amyloid precursor protein catabolic process / membrane protein ectodomain proteolysis / Collagen degradation / positive regulation of cyclin-dependent protein serine/threonine kinase activity / positive regulation of G1/S transition of mitotic cell cycle / positive regulation of blood vessel endothelial cell migration / Nuclear signaling by ERBB4 / Growth hormone receptor signaling / positive regulation of chemokine production / Notch signaling pathway / spleen development / Constitutive Signaling by NOTCH1 HD Domain Mutants / Activated NOTCH1 Transmits Signal to the Nucleus / B cell differentiation / PDZ domain binding / cell motility / negative regulation of transforming growth factor beta receptor signaling pathway / metalloendopeptidase activity / protein processing / Constitutive Signaling by NOTCH1 PEST Domain Mutants / Constitutive Signaling by NOTCH1 HD+PEST Domain Mutants / SH3 domain binding / metallopeptidase activity / actin cytoskeleton / integrin binding / T cell differentiation in thymus / peptidase activity / positive regulation of cell growth / endopeptidase activity / response to lipopolysaccharide / response to hypoxia / cell adhesion / positive regulation of cell migration / defense response to Gram-positive bacterium / response to xenobiotic stimulus / membrane raft / apical plasma membrane / endoplasmic reticulum lumen / Golgi membrane / positive regulation of cell population proliferation / cell surface / proteolysis / membrane / metal ion binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Metallo-peptidase family M12 / ADAM17, membrane-proximal domain / Membrane-proximal domain, switch, for ADAM17 / ADAM10/ADAM17 catalytic domain / Metallo-peptidase family M12B Reprolysin-like / Disintegrin / Disintegrin domain profile. / Homologues of snake disintegrins / Disintegrin domain / Disintegrin domain superfamily ...Metallo-peptidase family M12 / ADAM17, membrane-proximal domain / Membrane-proximal domain, switch, for ADAM17 / ADAM10/ADAM17 catalytic domain / Metallo-peptidase family M12B Reprolysin-like / Disintegrin / Disintegrin domain profile. / Homologues of snake disintegrins / Disintegrin domain / Disintegrin domain superfamily / Peptidase M12B, ADAM/reprolysin / ADAM type metalloprotease domain profile. / Collagenase (Catalytic Domain) / Collagenase (Catalytic Domain) / Metallopeptidase, catalytic domain superfamily / Neutral zinc metallopeptidases, zinc-binding region signature. / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-283 / Disintegrin and metalloproteinase domain-containing protein 17
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsWei, Y. / Rao, G.B. / Bandarage, U.K.
CitationJournal: Bioorg.Med.Chem.Lett. / Year: 2007
Title: Novel thiol-based TACE inhibitors: rational design, synthesis, and SAR of thiol-containing aryl sulfonamides
Authors: Govinda Rao, B. / Bandarage, U.K. / Wang, T. / Come, J.H. / Perola, E. / Wei, Y. / Tian, S.K. / Saunders, J.O.
History
DepositionJan 10, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 27, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 20, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: TNF- a Converting Enzyme (TACE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,4133
Polymers30,0371
Non-polymers3772
Water2,540141
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)56.550, 50.060, 42.980
Angle α, β, γ (deg.)90.000, 92.580, 90.000
Int Tables number4
Space group name H-MP1211
DetailsThere is one biological monomer in the crystallographic asymmetric unit.

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Components

#1: Protein TNF- a Converting Enzyme (TACE) / A disintegrin and metalloproteinase domain 17 / TNF-alpha-converting enzyme / TNF-alpha convertase ...A disintegrin and metalloproteinase domain 17 / TNF-alpha-converting enzyme / TNF-alpha convertase / Snake venom-like protease / CD156b antigen


Mass: 30036.664 Da / Num. of mol.: 1 / Fragment: TACE Proteinase domain (Residues 216-477) / Mutation: S266A, N452Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TACE / Plasmid: PBEV11TOPO / References: UniProt: P78536, ADAM 17 endopeptidase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-283 / (3S)-1-{[4-(BUT-2-YN-1-YLOXY)PHENYL]SULFONYL}PYRROLIDINE-3-THIOL


Mass: 311.420 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H17NO3S2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 141 / 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: 2.02 Å3/Da / Density % sol: 39.19 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 30% PGME 550, 0.1M BIS-TRIS, 50 mM CaCl2, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Feb 16, 2003 / Details: mirrors
RadiationMonochromator: Ni mirror + Ni filter / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionHighest resolution: 2 Å / Num. obs: 16132 / Observed criterion σ(F): 2 / Biso Wilson estimate: 12.2 Å2

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Processing

Software
NameVersionClassificationNB
AMoREphasing
CNSrefinement
PDB_EXTRACT2data extraction
CNX2005refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1BKC

1bkc


Resolution: 2→18.87 Å / Rfactor Rfree error: 0.01 / FOM work R set: 0.825 / Data cutoff high absF: 1522612.375 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.268 774 5 %RANDOM 5% of data
Rwork0.21 ---
obs0.213 15396 94 %-
all-15550 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 55.826 Å2 / ksol: 0.361 e/Å3
Displacement parametersBiso mean: 30.9 Å2
Baniso -1Baniso -2Baniso -3
1-7.87 Å20 Å28.38 Å2
2---2.83 Å20 Å2
3----5.04 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.31 Å0.24 Å
Luzzati d res low-5 Å
Luzzati sigma a0.27 Å0.33 Å
Refinement stepCycle: LAST / Resolution: 2→18.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2108 0 21 141 2270
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1
X-RAY DIFFRACTIONc_dihedral_angle_d22
X-RAY DIFFRACTIONc_improper_angle_d0.58
X-RAY DIFFRACTIONc_mcbond_it1.381.5
X-RAY DIFFRACTIONc_mcangle_it2.152
X-RAY DIFFRACTIONc_scbond_it2.132
X-RAY DIFFRACTIONc_scangle_it3.082.5
LS refinement shellResolution: 2→2.13 Å / Rfactor Rfree error: 0.032 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.341 115 5.1 %
Rwork0.308 2157 -
obs-2272 84.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2183.param183.top
X-RAY DIFFRACTION3water_rep.paramwater_rep.top
X-RAY DIFFRACTION4ion.paramion.top
X-RAY DIFFRACTION5parmxray.xpl

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