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- PDB-1tfq: NMR Structure of an Antagonists of the XIAP-Caspase-9 Interaction... -

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Basic information

Entry
Database: PDB / ID: 1tfq
TitleNMR Structure of an Antagonists of the XIAP-Caspase-9 Interaction Complexed to the BIR3 domain of XIAP
ComponentsBaculoviral IAP repeat-containing protein 4
KeywordsAPOPTOSIS / COMPLEX / ligand-PROTEIN / BIR / XIAP
Function / homology
Function and homology information


endopeptidase regulator activity / regulation of apoptosis involved in tissue homeostasis / inhibition of cysteine-type endopeptidase activity / positive regulation of protein linear polyubiquitination / regulation of BMP signaling pathway / copper ion homeostasis / nucleotide-binding oligomerization domain containing 1 signaling pathway / regulation of nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway / protein serine/threonine kinase binding / nucleotide-binding oligomerization domain containing 2 signaling pathway ...endopeptidase regulator activity / regulation of apoptosis involved in tissue homeostasis / inhibition of cysteine-type endopeptidase activity / positive regulation of protein linear polyubiquitination / regulation of BMP signaling pathway / copper ion homeostasis / nucleotide-binding oligomerization domain containing 1 signaling pathway / regulation of nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway / protein serine/threonine kinase binding / nucleotide-binding oligomerization domain containing 2 signaling pathway / SMAC, XIAP-regulated apoptotic response / Regulation of the apoptosome activity / Activation of caspases through apoptosome-mediated cleavage / SMAC (DIABLO) binds to IAPs / SMAC(DIABLO)-mediated dissociation of IAP:caspase complexes / TNFR1-induced proapoptotic signaling / RIPK1-mediated regulated necrosis / regulation of innate immune response / cysteine-type endopeptidase inhibitor activity / protein K63-linked ubiquitination / cysteine-type endopeptidase inhibitor activity involved in apoptotic process / positive regulation of type I interferon production / negative regulation of tumor necrosis factor-mediated signaling pathway / Regulation of PTEN localization / TNFR1-induced NF-kappa-B signaling pathway / positive regulation of protein ubiquitination / Deactivation of the beta-catenin transactivating complex / Regulation of TNFR1 signaling / positive regulation of JNK cascade / RING-type E3 ubiquitin transferase / negative regulation of cysteine-type endopeptidase activity involved in apoptotic process / Regulation of necroptotic cell death / Wnt signaling pathway / Regulation of PTEN stability and activity / ubiquitin-protein transferase activity / positive regulation of canonical Wnt signaling pathway / ubiquitin protein ligase activity / regulation of cell population proliferation / regulation of inflammatory response / neuron apoptotic process / positive regulation of canonical NF-kappaB signal transduction / regulation of apoptotic process / regulation of cell cycle / defense response to bacterium / DNA damage response / negative regulation of apoptotic process / nucleoplasm / identical protein binding / metal ion binding / nucleus / cytosol / cytoplasm
Similarity search - Function
XIAP/BIRC8, UBA domain / : / BIRC2/3-like, UBA domain / Inhibitor Of Apoptosis Protein (2mihbC-IAP-1); Chain A / Inhibitor Of Apoptosis Protein (2mihbC-IAP-1); Chain A / BIR repeat. / BIR repeat / Inhibitor of Apoptosis domain / BIR repeat profile. / Baculoviral inhibition of apoptosis protein repeat ...XIAP/BIRC8, UBA domain / : / BIRC2/3-like, UBA domain / Inhibitor Of Apoptosis Protein (2mihbC-IAP-1); Chain A / Inhibitor Of Apoptosis Protein (2mihbC-IAP-1); Chain A / BIR repeat. / BIR repeat / Inhibitor of Apoptosis domain / BIR repeat profile. / Baculoviral inhibition of apoptosis protein repeat / Zinc finger, C3HC4 type (RING finger) / Death-like domain superfamily / Ring finger / Zinc finger RING-type profile. / Zinc finger, RING-type / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-998 / E3 ubiquitin-protein ligase XIAP
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
Model type detailsminimized average
AuthorsOost, T.K. / Sun, C. / Armstrong, R.C. / Al-Assaad, A.S. / Betz, S.F. / Deckwerth, T.L. / Elmore, S.W. / Meadows, R.P. / Olejniczak, E.T. / Oleksijew, A. ...Oost, T.K. / Sun, C. / Armstrong, R.C. / Al-Assaad, A.S. / Betz, S.F. / Deckwerth, T.L. / Elmore, S.W. / Meadows, R.P. / Olejniczak, E.T. / Oleksijew, A. / Oltersdorf, T. / Rosenberg, S.H. / Shoemaker, A.R. / Zou, H. / Fesik, S.W.
CitationJournal: J.Med.Chem. / Year: 2004
Title: Discovery of Potent Antagonists of the Antiapoptotic Protein XIAP for the Treatment of Cancer.
Authors: Oost, T.K. / Sun, C. / Armstrong, R.C. / Al-Assaad, A.S. / Betz, S.F. / Deckwerth, T.L. / Ding, H. / Elmore, S.W. / Meadows, R.P. / Olejniczak, E.T. / Oleksijew, A. / Oltersdorf, T. / ...Authors: Oost, T.K. / Sun, C. / Armstrong, R.C. / Al-Assaad, A.S. / Betz, S.F. / Deckwerth, T.L. / Ding, H. / Elmore, S.W. / Meadows, R.P. / Olejniczak, E.T. / Oleksijew, A. / Oltersdorf, T. / Rosenberg, S.H. / Shoemaker, A.R. / Tomaselli, K.J. / Zou, H. / Fesik, S.W.
History
DepositionMay 27, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 7, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 2, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly ...database_2 / pdbx_struct_assembly / pdbx_struct_conn_angle / pdbx_struct_oper_list / 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_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_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Baculoviral IAP repeat-containing protein 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,9333
Polymers13,4251
Non-polymers5082
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)1 / -
RepresentativeModel #1minimized average structure

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Components

#1: Protein Baculoviral IAP repeat-containing protein 4 / Inhibitor of apoptosis protein 3 / X-linked inhibitor of apoptosis protein / XIAP / X-linked IAP / ...Inhibitor of apoptosis protein 3 / X-linked inhibitor of apoptosis protein / XIAP / X-linked IAP / IAP-like protein / HILP


Mass: 13424.951 Da / Num. of mol.: 1 / Fragment: BIR3 of XIAP: RESIDUES 241-356
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BIRC4, API3, IAP3, XIAP / Plasmid: pet28b / Production host: Escherichia coli (E. coli) / References: UniProt: P98170
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-998 / N-METHYLALANYL-3-METHYLVALYL-N-(1,2,3,4-TETRAHYDRONAPHTHALEN-1-YL)PROLINAMIDE / 1-[3,3-DIMETHYL-2-(2-METHYLAMINO-PROPIONYLAMINO)-BUTYRYL]-PYRROLIDINE-2-CARBOXYLIC ACID(1,2,3,4-TETRAHYDRO-NAPHTHALEN-1-YL)-AMIDE


Mass: 442.594 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C25H38N4O3

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 13C-separated NOESY
1213D 15N-separated NOESY
1312D 13C,15N filtered NOESY
1412D 13C,15N filtered TOCSY
1513D 13C,15N filtered ,13C separated NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
1U-15N, 0.8mM Bir3,20mM Tris, 2mMDTT, 20mM phosphate buffer, 120mM NaCl, 90%H2O, 10%D2090%H2O, 10%D20
2U-15N,13C 0.8mM Bir3, 20mM Tris, 2mMDTT, 20mM phosphate buffer, 120mM NaCl, 100%D2O100% D2O
Sample conditionsIonic strength: 20mM Tris / pH: 7.2 / Pressure: ambient / Temperature: 303 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Bruker DRX / Manufacturer: Bruker / Model: DRX / Field strength: 600 MHz

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Processing

NMR softwareName: CNS / Version: 2000 / Developer: Brunger / Classification: refinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: minimized average structure
NMR ensembleConformers submitted total number: 1

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