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- PDB-1bkc: CATALYTIC DOMAIN OF TNF-ALPHA CONVERTING ENZYME (TACE) -

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Basic information

Entry
Database: PDB / ID: 1bkc
TitleCATALYTIC DOMAIN OF TNF-ALPHA CONVERTING ENZYME (TACE)
Components(TUMOR NECROSIS FACTOR-ALPHA-CONVERTING ...) x 3
KeywordsZN-ENDOPEPTIDASE / HYDROLASE / TNF-ALPHA
Function / homology
Function and homology information


ADAM 17 endopeptidase / regulation of mast cell apoptotic process / : / signal release / metalloendopeptidase activity involved in amyloid precursor protein catabolic process / cellular response to high density lipoprotein particle stimulus / production of molecular mediator involved in inflammatory response / Constitutive Signaling by NOTCH1 t(7;9)(NOTCH1:M1580_K2555) Translocation Mutant / Notch receptor processing / interleukin-6 receptor binding ...ADAM 17 endopeptidase / regulation of mast cell apoptotic process / : / signal release / metalloendopeptidase activity involved in amyloid precursor protein catabolic process / cellular response to high density lipoprotein particle stimulus / production of molecular mediator involved in inflammatory response / 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 / cytokine precursor processing / positive regulation of leukocyte chemotaxis / regulation of axon regeneration / metallodipeptidase activity / Release of Hh-Np from the secreting cell / Regulated proteolysis of p75NTR / commissural neuron axon guidance / regulation of neuron migration / positive regulation of tumor necrosis factor-mediated signaling pathway / neutrophil mediated immunity / 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 / 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 / Activated NOTCH1 Transmits Signal to the Nucleus / B cell differentiation / PDZ domain binding / phosphatidylinositol 3-kinase/protein kinase B signal transduction / cell motility / negative regulation of transforming growth factor beta receptor signaling pathway / metalloendopeptidase activity / protein processing / SH3 domain binding / Constitutive Signaling by NOTCH1 PEST Domain Mutants / Constitutive Signaling by NOTCH1 HD+PEST Domain Mutants / integrin binding / epidermal growth factor receptor signaling pathway / metallopeptidase activity / positive regulation of tumor necrosis factor production / T cell differentiation in thymus / peptidase activity / actin cytoskeleton / negative regulation of neuron projection development / positive regulation of cell growth / response to lipopolysaccharide / endopeptidase activity / response to hypoxia / cell adhesion / defense response to Gram-positive bacterium / positive regulation of cell migration / apical plasma membrane / membrane raft / response to xenobiotic stimulus / endoplasmic reticulum lumen / Golgi membrane / positive regulation of cell population proliferation / cell surface / proteolysis / metal ion binding / membrane / plasma membrane / cytoplasm / cytosol
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 / Disintegrin and metalloproteinase domain-containing protein 17
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MULTIWAVELENGTH ANOMALOUS DISPERSION / Resolution: 2 Å
AuthorsMaskos, K. / Fernandez-Catalan, C. / Bode, W.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 1998
Title: Crystal structure of the catalytic domain of human tumor necrosis factor-alpha-converting enzyme.
Authors: Maskos, K. / Fernandez-Catalan, C. / Huber, R. / Bourenkov, G.P. / Bartunik, H. / Ellestad, G.A. / Reddy, P. / Wolfson, M.F. / Rauch, C.T. / Castner, B.J. / Davis, R. / Clarke, H.R. / ...Authors: Maskos, K. / Fernandez-Catalan, C. / Huber, R. / Bourenkov, G.P. / Bartunik, H. / Ellestad, G.A. / Reddy, P. / Wolfson, M.F. / Rauch, C.T. / Castner, B.J. / Davis, R. / Clarke, H.R. / Petersen, M. / Fitzner, J.N. / Cerretti, D.P. / March, C.J. / Paxton, R.J. / Black, R.A. / Bode, W.
History
DepositionApr 23, 1998Processing site: BNL
Revision 1.0Jun 22, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Feb 27, 2013Group: Other
Revision 1.4Nov 3, 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_asym_id / _struct_conn.ptnr1_label_asym_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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Nov 6, 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

Downloads & links

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Assembly

Deposited unit
A: TUMOR NECROSIS FACTOR-ALPHA-CONVERTING ENZYME
C: TUMOR NECROSIS FACTOR-ALPHA-CONVERTING ENZYME
E: TUMOR NECROSIS FACTOR-ALPHA-CONVERTING ENZYME
I: TUMOR NECROSIS FACTOR-ALPHA-CONVERTING ENZYME
hetero molecules


Theoretical massNumber of molelcules
Total (without water)117,77212
Polymers115,8484
Non-polymers1,9248
Water29,1841620
1
A: TUMOR NECROSIS FACTOR-ALPHA-CONVERTING ENZYME
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,4353
Polymers28,9541
Non-polymers4812
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
E: TUMOR NECROSIS FACTOR-ALPHA-CONVERTING ENZYME
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,4513
Polymers28,9701
Non-polymers4812
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: TUMOR NECROSIS FACTOR-ALPHA-CONVERTING ENZYME
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,4353
Polymers28,9541
Non-polymers4812
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
I: TUMOR NECROSIS FACTOR-ALPHA-CONVERTING ENZYME
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,4493
Polymers28,9681
Non-polymers4812
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)61.380, 126.270, 81.270
Angle α, β, γ (deg.)90.00, 107.41, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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TUMOR NECROSIS FACTOR-ALPHA-CONVERTING ... , 3 types, 4 molecules ACEI

#1: Protein TUMOR NECROSIS FACTOR-ALPHA-CONVERTING ENZYME / TACE


Mass: 28954.457 Da / Num. of mol.: 2 / Mutation: S266A, N452Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / References: UniProt: P78536
#2: Protein TUMOR NECROSIS FACTOR-ALPHA-CONVERTING ENZYME / TACE


Mass: 28970.480 Da / Num. of mol.: 1 / Mutation: S266A, N452Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / References: UniProt: P78536
#3: Protein TUMOR NECROSIS FACTOR-ALPHA-CONVERTING ENZYME / TACE


Mass: 28968.484 Da / Num. of mol.: 1 / Mutation: S266A, N452Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / References: UniProt: P78536

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Non-polymers , 3 types, 1628 molecules

#4: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#5: 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.: 4 / 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
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1620 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.59 Å3/Da / Density % sol: 52.6 %
Crystal growpH: 5.4 / Details: pH 5.4
Crystal grow
*PLUS
Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
120 %isopropanol1reservoir
220 %PEG40001reservoir
30.1 Mcitrate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MPG/DESY, HAMBURG / Beamline: BW6 / Wavelength: 1.2776
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Aug 1, 1997 / Details: MIRRORS
RadiationMonochromator: NI FILTER / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.2776 Å / Relative weight: 1
ReflectionResolution: 2→20 Å / Num. obs: 77653 / % possible obs: 96.9 % / Observed criterion σ(I): 2 / Redundancy: 5 % / Rmerge(I) obs: 0.031
Reflection shellResolution: 2→2 Å

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CCP4model building
REFMACrefinement
CCP4phasing
RefinementMethod to determine structure: MULTIWAVELENGTH ANOMALOUS DISPERSION
Resolution: 2→12 Å /
RfactorNum. reflection
Rfree0.27 -
Rwork0.18 -
obs-71400
Refinement stepCycle: LAST / Resolution: 2→12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8082 0 120 1620 9822

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