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- PDB-2i47: Crystal structure of catalytic domain of TACE with inhibitor -

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Basic information

Entry
Database: PDB / ID: 2i47
TitleCrystal structure of catalytic domain of TACE with inhibitor
ComponentsADAM 17
KeywordsHYDROLASE / TACE/ADAM-17 / TACE-inhibitor complex
Function / homology
Function and homology information


ADAM 17 endopeptidase / regulation of mast cell apoptotic process / signal release / positive regulation of epidermal growth factor-activated receptor activity / metalloendopeptidase activity involved in amyloid precursor protein catabolic process / cellular response to high density lipoprotein particle stimulus / Constitutive Signaling by NOTCH1 t(7;9)(NOTCH1:M1580_K2555) Translocation Mutant / Notch receptor processing / interleukin-6 receptor binding / tumor necrosis factor binding ...ADAM 17 endopeptidase / regulation of mast cell apoptotic process / signal release / positive regulation of epidermal growth factor-activated receptor activity / metalloendopeptidase activity involved in amyloid precursor protein catabolic process / cellular response to high density lipoprotein particle stimulus / 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 / Release of Hh-Np from the secreting cell / Regulated proteolysis of p75NTR / commissural neuron axon guidance / neutrophil mediated immunity / positive regulation of tumor necrosis factor-mediated signaling pathway / germinal center formation / Notch binding / wound healing, spreading of epidermal cells / positive regulation of vascular endothelial cell proliferation / negative regulation of cold-induced thermogenesis / CD163 mediating an anti-inflammatory response / positive regulation of epidermal growth factor receptor signaling pathway / cell adhesion mediated by integrin / Signaling by EGFR / amyloid precursor protein catabolic process / cytokine binding / Collagen degradation / membrane protein ectodomain proteolysis / positive regulation of blood vessel endothelial cell migration / positive regulation of G1/S transition of mitotic cell cycle / positive regulation of cyclin-dependent protein serine/threonine kinase activity / Growth hormone receptor signaling / Nuclear signaling by ERBB4 / positive regulation of chemokine production / spleen development / Notch signaling pathway / Constitutive Signaling by NOTCH1 HD Domain Mutants / B cell differentiation / Activated NOTCH1 Transmits Signal to the Nucleus / PDZ domain binding / cell motility / negative regulation of transforming growth factor beta receptor signaling pathway / protein processing / metalloendopeptidase activity / SH3 domain binding / Constitutive Signaling by NOTCH1 PEST Domain Mutants / Constitutive Signaling by NOTCH1 HD+PEST Domain Mutants / positive regulation of tumor necrosis factor production / metallopeptidase activity / integrin binding / actin cytoskeleton / peptidase activity / T cell differentiation in thymus / positive regulation of cell growth / endopeptidase activity / response to lipopolysaccharide / response to hypoxia / cell adhesion / defense response to Gram-positive bacterium / positive regulation of cell migration / membrane raft / response to xenobiotic stimulus / 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
ADAM17, membrane-proximal domain / Membrane-proximal domain, switch, for ADAM17 / Metallo-peptidase family M12 / ADAM10/ADAM17 catalytic domain / : / Disintegrin / Disintegrin domain profile. / Homologues of snake disintegrins / Disintegrin domain / Disintegrin domain superfamily ...ADAM17, membrane-proximal domain / Membrane-proximal domain, switch, for ADAM17 / Metallo-peptidase family M12 / ADAM10/ADAM17 catalytic domain / : / 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
3,N(D,L-[2-(HYDROXYAMINO-CARBONYL)METHYL]-4-METHYL PENTANOYL)L-3-(TERT-BUTYL)GLYCYL-L-ALANINE / Chem-INN / Chem-KGY / Disintegrin and metalloproteinase domain-containing protein 17
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsXu, W. / Condon, J.S. / Lovering, F.E.
CitationJournal: Bioorg.Med.Chem.Lett. / Year: 2007
Title: Identification of potent and selective TACE inhibitors via the S1 pocket.
Authors: Condon, J.S. / Joseph-McCarthy, D. / Levin, J.I. / Lombart, H.G. / Lovering, F.E. / Sun, L. / Wang, W. / Xu, W. / Zhang, Y.
History
DepositionAug 21, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 5, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Feb 27, 2013Group: Other
Revision 1.4Oct 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 1.5Oct 16, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ADAM 17
B: ADAM 17
C: ADAM 17
D: ADAM 17
hetero molecules


Theoretical massNumber of molelcules
Total (without water)132,49712
Polymers130,3534
Non-polymers2,1448
Water12,899716
1
A: ADAM 17
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,0693
Polymers32,5881
Non-polymers4812
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: ADAM 17
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,0693
Polymers32,5881
Non-polymers4812
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: ADAM 17
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,1793
Polymers32,5881
Non-polymers5912
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: ADAM 17
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,1793
Polymers32,5881
Non-polymers5912
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)61.775, 126.193, 81.224
Angle α, β, γ (deg.)90.00, 107.41, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 32588.369 Da / Num. of mol.: 4 / Fragment: catalytic domain / Mutation: S266A, N452Q / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P78536, ADAM 17 endopeptidase
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-INN / N-{(2R)-2-[2-(hydroxyamino)-2-oxoethyl]-4-methylpentanoyl}-3-methyl-L-valyl-N-(2-aminoethyl)-L-alaninamide


Type: peptide-like, Peptide-like / Class: Enzyme inhibitor / Mass: 415.528 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C19H37N5O5
References: 3,N(D,L-[2-(HYDROXYAMINO-CARBONYL)METHYL]-4-METHYL PENTANOYL)L-3-(TERT-BUTYL)GLYCYL-L-ALANINE
#4: Chemical ChemComp-KGY / 4-({[4-(BUT-2-YN-1-YLOXY)PHENYL]SULFONYL}METHYL)-1-[(3,5-DIMETHYLISOXAZOL-4-YL)SULFONYL]-N-HYDROXYPIPERIDINE-4-CARBOXAMIDE


Mass: 525.595 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C22H27N3O8S2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 716 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.32 Å3/Da / Density % sol: 46.9 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 5.4
Details: 20% PEG4000, 20% isopropanol, 0.1M sodium Citrate, pH 5.4, VAPOR DIFFUSION, SITTING DROP, temperature 292K

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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 315 / Detector: CCD / Date: Mar 11, 2004
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. all: 107642 / Num. obs: 105942 / % possible obs: 98.4 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellResolution: 1.8→1.86 Å / % possible all: 91.1

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Processing

Software
NameVersionClassification
HKL-2000data collection
AMoREphasing
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→20 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.2271 4528 random
Rwork0.1982 --
obs0.1982 89581 -
all-93200 -
Refinement stepCycle: LAST / Resolution: 1.9→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8078 0 132 716 8926
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_d1.6
X-RAY DIFFRACTIONc_bond_deg0.01
LS refinement shellResolution: 1.9→1.91 Å
RfactorNum. reflection
Rfree0.2599 67
Rwork0.2542 -
obs-1533

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