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- PDB-1ft4: PHOTOCHEMICALLY-ENHANCED BINDING OF SMALL MOLECULES TO THE TUMOR ... -

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Basic information

Entry
Database: PDB / ID: 1ft4
TitlePHOTOCHEMICALLY-ENHANCED BINDING OF SMALL MOLECULES TO THE TUMOR NECROSIS FACTOR RECEPTOR-1
ComponentsSOLUBLE TUMOR NECROSIS FACTOR RECEPTOR 1
KeywordsSIGNALING PROTEIN / BINDING PROTEIN / CYTOKINE
Function / homology
Function and homology information


positive regulation of amide metabolic process / tumor necrosis factor receptor superfamily complex / pulmonary valve development / positive regulation of lipid metabolic process / aortic valve development / tumor necrosis factor receptor activity / negative regulation of extracellular matrix constituent secretion / positive regulation of apoptotic process involved in morphogenesis / regulation of membrane lipid metabolic process / TNFs bind their physiological receptors ...positive regulation of amide metabolic process / tumor necrosis factor receptor superfamily complex / pulmonary valve development / positive regulation of lipid metabolic process / aortic valve development / tumor necrosis factor receptor activity / negative regulation of extracellular matrix constituent secretion / positive regulation of apoptotic process involved in morphogenesis / regulation of membrane lipid metabolic process / TNFs bind their physiological receptors / tumor necrosis factor binding / negative regulation of cardiac muscle hypertrophy / TNF signaling / regulation of establishment of endothelial barrier / regulation of tumor necrosis factor-mediated signaling pathway / TNFR1-mediated ceramide production / TNFR1-induced proapoptotic signaling / prostaglandin metabolic process / Interleukin-10 signaling / extrinsic apoptotic signaling pathway via death domain receptors / positive regulation of execution phase of apoptosis / cell surface receptor signaling pathway via JAK-STAT / tumor necrosis factor-mediated signaling pathway / TNFR1-induced NF-kappa-B signaling pathway / protein localization to plasma membrane / Regulation of TNFR1 signaling / cellular response to mechanical stimulus / negative regulation of inflammatory response / cytokine-mediated signaling pathway / intrinsic apoptotic signaling pathway in response to DNA damage / positive regulation of inflammatory response / signaling receptor activity / transcription by RNA polymerase II / positive regulation of canonical NF-kappaB signal transduction / receptor complex / defense response to bacterium / membrane raft / inflammatory response / Golgi membrane / cell surface / positive regulation of transcription by RNA polymerase II / extracellular space / extracellular region / membrane / plasma membrane
Similarity search - Function
Tumour necrosis factor receptor 1A / Tumor necrosis factor receptor 1A, N-terminal / Tumor necrosis factor receptor 1A, death domain / : / Tumor Necrosis Factor Receptor, subunit A, domain 2 / Tumor Necrosis Factor Receptor, subunit A; domain 2 / TNFR/NGFR family cysteine-rich region domain profile. / TNFR/NGFR cysteine-rich region / TNFR/NGFR family cysteine-rich region signature. / Tumor necrosis factor receptor / nerve growth factor receptor repeats. ...Tumour necrosis factor receptor 1A / Tumor necrosis factor receptor 1A, N-terminal / Tumor necrosis factor receptor 1A, death domain / : / Tumor Necrosis Factor Receptor, subunit A, domain 2 / Tumor Necrosis Factor Receptor, subunit A; domain 2 / TNFR/NGFR family cysteine-rich region domain profile. / TNFR/NGFR cysteine-rich region / TNFR/NGFR family cysteine-rich region signature. / Tumor necrosis factor receptor / nerve growth factor receptor repeats. / TNFR/NGFR cysteine-rich region / Death domain profile. / DEATH domain, found in proteins involved in cell death (apoptosis). / Death domain / Death domain / Death-like domain superfamily / Ribbon / Mainly Beta
Similarity search - Domain/homology
Chem-703 / Tumor necrosis factor receptor superfamily member 1A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.9 Å
AuthorsMuckelbauer, J.K. / Chang, C.-H.
Citation
Journal: Proc.Natl.Acad.Sci.USA / Year: 2001
Title: Photochemically enhanced binding of small molecules to the tumor necrosis factor receptor-1 inhibits the binding of TNF-alpha.
Authors: Carter, P.H. / Scherle, P.A. / Muckelbauer, J.K. / Voss, M.E. / Liu, R.Q. / Thompson, L.A. / Tebben, A.J. / Solomon, K.A. / Lo, Y.C. / Li, Z. / Strzemienski, P. / Yang, G. / Falahatpisheh, N. ...Authors: Carter, P.H. / Scherle, P.A. / Muckelbauer, J.K. / Voss, M.E. / Liu, R.Q. / Thompson, L.A. / Tebben, A.J. / Solomon, K.A. / Lo, Y.C. / Li, Z. / Strzemienski, P. / Yang, G. / Falahatpisheh, N. / Xu, M. / Wu, Z. / Farrow, N.A. / Ramnarayan, K. / Wang, J. / Rideout, D. / Yalamoori, V. / Domaille, P. / Underwood, D.J. / Trzaskos, J.M. / Friedman, S.M. / Newton, R.C. / Decicco, C.P. / Muckelbauer, J.A.
#1: Journal: J.Biol.Chem. / Year: 1995
Title: Crystallographic Evidence for Dimerization of Unliganded Tumor Necrosis Factor Receptor
Authors: Naismith, J.H. / Devine, T.Q. / Brandhuber, B.J. / Sprang, S.R.
#2: Journal: Cell(Cambridge,Mass.) / Year: 1993
Title: Crystal Structure of the Soluble Human 55 Kd Tnf Receptor-Human Tnfb Complex: Implication for Tnf Receptor Activation
Authors: Banner, D.W. / D'Arcy, A. / Janes, W. / Gentz, W. / Schoenfeld, H.-J. / Broger, C. / Loetscher, H. / Lesslauer, W.
History
DepositionSep 11, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 12, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software
Revision 1.4Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _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_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

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Assembly

Deposited unit
A: SOLUBLE TUMOR NECROSIS FACTOR RECEPTOR 1
B: SOLUBLE TUMOR NECROSIS FACTOR RECEPTOR 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,1283
Polymers36,6722
Non-polymers4571
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)67.800, 67.800, 190.000
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Cell settingtetragonal
Space group name H-MP41212

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Components

#1: Protein SOLUBLE TUMOR NECROSIS FACTOR RECEPTOR 1 / TUMOR NECROSIS FACTOR / BINDING PROTEIN 1 / TBPI / P60 / TNF-R1 / TNF-RI / P55


Mass: 18335.830 Da / Num. of mol.: 2
Fragment: 55 KD EXTRACELLULAR DOMAIN (MET PLUS RESIDUES 12-272)
Source method: isolated from a genetically manipulated source
Details: N OF ALA 62, CHAIN A IS BOUND TO LIGAND 705 / Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P19438
#2: Chemical ChemComp-703 / 5-(3-MORPHOLIN-4-YL-PROPYL)-2-(3-NITRO-PHENYL)-4-THIOXO-4,5-DIHYDRO-1-THIA-3B,5-DIAZA-CYCLOPENTA[A]PENTALEN-6-ONE / 6-[3-(4-MORPHOLINYL)PROPYL]-2-(3-NITROPHENYL)-5-THIOXO-5,6,-DIHYDRO-7H-THIENOL[2',3':4,5]PYRROLO[1,2-C] IMIDAZOL-7-ONE


Mass: 456.538 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H20N4O4S2
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: 2.98 Å3/Da / Density % sol: 58.67 %
Crystal growTemperature: 297 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: MPD, Ammonium Acetate Tris Buffer, pH 8.5, VAPOR DIFFUSION, SITTING DROP at 297K
Crystal grow
*PLUS
Temperature: 293 K / Details: Rodseth, L.E., (1994) J.Mol.Biol., 239, 332.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
11.6 mg/mlprotein1drop
225 %(v/v)MPD1drop
350 mMTris-HCl1drop
40.1 %(w/v)beta-octylglucoside1drop
5100 mM1dropNaCl
6250 mMammonium acetate1drop
754 %MPD1reservoir
8100 mMTris-HCl1reservoir
9500 mMammonium acetate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 5ID-B / Wavelength: 1
DetectorType: MARRESEARCH / Detector: CCD / Date: Feb 13, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.9→35 Å / Num. obs: 9191 / % possible obs: 88 % / Rmerge(I) obs: 0.093 / Net I/σ(I): 17

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
EPMRphasing
X-PLOR3.851refinement
RefinementResolution: 2.9→10 Å / σ(F): 2 /
RfactorNum. reflection
Rwork0.274 -
all0.275 8247
Refinement stepCycle: LAST / Resolution: 2.9→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2733 0 31 0 2764
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.013
X-RAY DIFFRACTIONx_angle_deg3.1
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 10 Å / σ(F): 2 / Rfactor obs: 0.274
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: x_angle_deg / Dev ideal: 3.1

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