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- PDB-3g42: Crystal Structure of TACE with Tryptophan Sulfonamide Derivative ... -

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Basic information

Entry
Database: PDB / ID: 3g42
TitleCrystal Structure of TACE with Tryptophan Sulfonamide Derivative Inhibitor
ComponentsADAM 17
KeywordsHYDROLASE / TACE/ADAM-17 / TACE-inhibitor complex / Zn-endopeptidase / Alternative splicing / Cleavage on pair of basic residues / Glycoprotein / Membrane / Metal-binding / Metalloprotease / Notch signaling pathway / Phosphoprotein / Polymorphism / Protease / SH3-binding / Transmembrane / Zinc / Zymogen
Function / homology
Function and homology information


Metallo-peptidase family M12 / Domain of unknown function DUF3850 / Domain of unknown function (DUF3850) / ASCH / ASCH domain / Collagenase (Catalytic Domain) / Collagenase (Catalytic Domain) / PUA-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-792 / DUF3850 domain-containing protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsXu, W. / Park, K. / Gopalsamy, A. / Aplasca, A. / Zhang, Y.H. / Levin, J.I.
CitationJournal: Bioorg.Med.Chem. / Year: 2009
Title: Synthesis and activity of tryptophan sulfonamide derivatives as novel non-hydroxamate TNF-alpha converting enzyme (TACE) inhibitors.
Authors: Park, K. / Gopalsamy, A. / Aplasca, A. / Ellingboe, J.W. / Xu, W. / Zhang, Y. / Levin, J.I.
History
DepositionFeb 3, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 19, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
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_label_asym_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 1.4Sep 6, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.5Oct 9, 2024Group: Structure summary / Category: 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: ADAM 17
B: ADAM 17
C: ADAM 17
D: ADAM 17
hetero molecules


Theoretical massNumber of molelcules
Total (without water)132,32112
Polymers130,3534
Non-polymers1,9688
Water7,909439
1
A: ADAM 17
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,0803
Polymers32,5881
Non-polymers4922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: ADAM 17
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,0803
Polymers32,5881
Non-polymers4922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: ADAM 17
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,0803
Polymers32,5881
Non-polymers4922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: ADAM 17
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,0803
Polymers32,5881
Non-polymers4922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)163.846, 51.330, 132.741
Angle α, β, γ (deg.)90.00, 102.64, 90.00
Int Tables number5
Space group name H-MC121

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Components

#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: 32588.369 Da / Num. of mol.: 4 / Fragment: catalytic domain / Mutation: S266A, N452Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ADAM17, CSVP, TACE / Cell line (production host): CHO cell lines / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: P78536, EC: 3.4.24.86
#2: Chemical
ChemComp-792 / N-{[4-(but-2-yn-1-yloxy)phenyl]sulfonyl}-5-methyl-D-tryptophan


Mass: 426.485 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C22H22N2O5S
#3: Chemical
ChemComp-ZN / ZINC ION


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


Mass: 18.015 Da / Num. of mol.: 439 / 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: 2.09 Å3/Da / Density % sol: 41.12 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 5.4
Details: PEG4k, isopropanol, NaCitrate, pH 5.4, VAPOR DIFFUSION, SITTING DROP, temperature 292K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Nov 15, 2002 / Details: Yale Mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.1→20 Å / Num. all: 63380 / Num. obs: 62447 / % possible obs: 98.5 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3 / Rmerge(I) obs: 0.048 / Rsym value: 0.048
Reflection shellResolution: 2.1→2.14 Å / Rmerge(I) obs: 0.162 / Mean I/σ(I) obs: 8.13 / % possible all: 98.8

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Processing

Software
NameVersionClassification
HKL-2000data collection
AMoREphasing
X-PLOR3.851refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1ZXC

1zxc


Resolution: 2.1→20 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2567 933 -random
Rwork0.2183 ---
all0.2183 63380 --
obs-62447 98.5 %-
Refinement stepCycle: LAST / Resolution: 2.1→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8080 0 123 439 8642
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.006
X-RAY DIFFRACTIONx_angle_deg1.292
LS refinement shellResolution: 2.1→2.11 Å
RfactorNum. reflection
Rfree0.231 66
Rwork0.2277 -
obs-1105

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