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- PDB-3edz: Crystal structure of catalytic domain of TACE with hydroxamate in... -

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Basic information

Entry
Database: PDB / ID: 3edz
TitleCrystal structure of catalytic domain of TACE with hydroxamate inhibitor
ComponentsADAM 17
KeywordsHYDROLASE / ZN-ENDOPEPTIDASE / Cleavage on pair of basic residues / Glycoprotein / Membrane / Metal-binding / Metalloprotease / Notch signaling pathway / Phosphoprotein / Protease / SH3-binding / Transmembrane / Zymogen
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 / 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 / wound healing, spreading of epidermal cells / Notch binding / negative regulation of cold-induced thermogenesis / positive regulation of leukocyte chemotaxis / CD163 mediating an anti-inflammatory response / positive regulation of vascular endothelial cell proliferation / positive regulation of epidermal growth factor receptor signaling pathway / cell adhesion mediated by integrin / 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 / Growth hormone receptor signaling / Nuclear signaling by ERBB4 / 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 / protein processing / metalloendopeptidase activity / 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 / apical plasma membrane / membrane raft / 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
3,N(D,L-[2-(HYDROXYAMINO-CARBONYL)METHYL]-4-METHYL PENTANOYL)L-3-(TERT-BUTYL)GLYCYL-L-ALANINE / Chem-550 / CITRIC ACID / Chem-INN / Disintegrin and metalloproteinase domain-containing protein 17
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / PDB entry 1bkc / Resolution: 1.9 Å
AuthorsMazzola, R.D. / Zhu, Z. / Sinning, L. / McKittrick, B. / Lavey, B. / Spitler, J. / Kozlowski, J. / Neng-Yang, S. / Zhou, G. / Guo, Z. ...Mazzola, R.D. / Zhu, Z. / Sinning, L. / McKittrick, B. / Lavey, B. / Spitler, J. / Kozlowski, J. / Neng-Yang, S. / Zhou, G. / Guo, Z. / Orth, P. / Madison, V. / Sun, J. / Lundell, D. / Niu, X.
CitationJournal: Bioorg.Med.Chem.Lett. / Year: 2008
Title: Discovery of novel hydroxamates as highly potent tumor necrosis factor-alpha converting enzyme inhibitors. Part II: optimization of the S3' pocket.
Authors: Mazzola, R.D. / Zhu, Z. / Sinning, L. / McKittrick, B. / Lavey, B. / Spitler, J. / Kozlowski, J. / Neng-Yang, S. / Zhou, G. / Guo, Z. / Orth, P. / Madison, V. / Sun, J. / Lundell, D. / Niu, X.
History
DepositionSep 3, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 23, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Feb 27, 2013Group: Other
Revision 1.3Oct 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_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 / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)62,6888
Polymers61,3372
Non-polymers1,3516
Water7,710428
1
A: ADAM 17
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,3414
Polymers30,6681
Non-polymers6733
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: ADAM 17
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,3464
Polymers30,6681
Non-polymers6783
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)74.796, 75.702, 102.877
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein ADAM 17 / / 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


Mass: 30668.264 Da / Num. of mol.: 2 / Fragment: UNP residues 215-477 / Mutation: S266A, V353G, N452Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ADAM17, CSVP, TACE / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P78536, ADAM 17 endopeptidase

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Non-polymers , 5 types, 434 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / 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.: 1 / 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-CIT / CITRIC ACID / Citric acid


Mass: 192.124 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H8O7
#5: Chemical ChemComp-550 / methyl (1R,2S)-2-(hydroxycarbamoyl)-1-{4-[(2-methylquinolin-4-yl)methoxy]benzyl}cyclopropanecarboxylate


Mass: 420.458 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H24N2O5
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 428 / 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: 2.37 Å3/Da / Density % sol: 48.19 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 15% PEG 6000, 10% 2-Propanol, 100 mM sodium citrate buffer, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Aug 3, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→30 Å / Num. obs: 42913 / % possible obs: 92 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 25.287 Å2 / Rmerge(I) obs: 0.043
Reflection shellResolution: 1.9→2 Å / % possible all: 69.6

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
AMoREphasing
BUSTER-TNT2.1.1refinement
DENZOdata reduction
HKL-2000data scaling
RefinementMethod to determine structure: PDB entry 1bkc / Resolution: 1.9→28.83 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2043 823 1.92 %RANDOM
Rwork0.1737 ---
obs0.1743 42913 84.6 %-
Displacement parametersBiso mean: 29.47 Å2
Baniso -1Baniso -2Baniso -3
1--0.69016127 Å20 Å20 Å2
2--0.50377432 Å20 Å2
3---0.18638695 Å2
Refinement stepCycle: LAST / Resolution: 1.9→28.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4051 0 88 428 4567
Refine LS restraints
Refine-IDTypeDev idealNumberWeight
X-RAY DIFFRACTIONt_bond_d0.00742472
X-RAY DIFFRACTIONt_angle_deg1.01957192
X-RAY DIFFRACTIONt_dihedral_angle_d15.7038640
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes0.0081342
X-RAY DIFFRACTIONt_gen_planes0.0156065
X-RAY DIFFRACTIONt_it1.486421920
X-RAY DIFFRACTIONt_nbd0.042565
LS refinement shellResolution: 1.9→2.07 Å / Total num. of bins used: 5
RfactorNum. reflection% reflection
Rfree0.235 160 1.94 %
Rwork0.1843 8083 -
all0.1852 8243 -
obs--84.6 %

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