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- PDB-6w74: Structure of cIAP with compound 15 -

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Basic information

Entry
Database: PDB / ID: 6w74
TitleStructure of cIAP with compound 15
ComponentsBaculoviral IAP repeat-containing protein 2
KeywordsLIGASE / cIAP E3 PROTAC
Function / homology
Function and homology information


negative regulation of ripoptosome assembly involved in necroptotic process / regulation of cysteine-type endopeptidase activity / FBXO family protein binding / regulation of RIG-I signaling pathway / positive regulation of protein K48-linked ubiquitination / regulation of non-canonical NF-kappaB signal transduction / TNF receptor superfamily (TNFSF) members mediating non-canonical NF-kB pathway / regulation of necroptotic process / regulation of nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway / positive regulation of protein K63-linked ubiquitination ...negative regulation of ripoptosome assembly involved in necroptotic process / regulation of cysteine-type endopeptidase activity / FBXO family protein binding / regulation of RIG-I signaling pathway / positive regulation of protein K48-linked ubiquitination / regulation of non-canonical NF-kappaB signal transduction / TNF receptor superfamily (TNFSF) members mediating non-canonical NF-kB pathway / regulation of necroptotic process / regulation of nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway / positive regulation of protein K63-linked ubiquitination / CD40 receptor complex / XY body / negative regulation of necroptotic process / regulation of reactive oxygen species metabolic process / positive regulation of protein monoubiquitination / TNFR1-induced proapoptotic signaling / RIPK1-mediated regulated necrosis / regulation of toll-like receptor signaling pathway / regulation of innate immune response / Apoptotic cleavage of cellular proteins / regulation of cell differentiation / non-canonical NF-kappaB signal transduction / necroptotic process / cysteine-type endopeptidase inhibitor activity involved in apoptotic process / canonical NF-kappaB signal transduction / response to cAMP / tumor necrosis factor-mediated signaling pathway / TICAM1, RIP1-mediated IKK complex recruitment / IKK complex recruitment mediated by RIP1 / TNFR1-induced NF-kappa-B signaling pathway / ubiquitin binding / positive regulation of protein ubiquitination / TNFR2 non-canonical NF-kB pathway / placenta development / Regulation of TNFR1 signaling / RING-type E3 ubiquitin transferase / NOD1/2 Signaling Pathway / Regulation of necroptotic cell death / cytoplasmic side of plasma membrane / protein polyubiquitination / ubiquitin-protein transferase activity / ubiquitin protein ligase activity / regulation of cell population proliferation / protein-folding chaperone binding / regulation of inflammatory response / transferase activity / regulation of apoptotic process / proteasome-mediated ubiquitin-dependent protein catabolic process / positive regulation of canonical NF-kappaB signal transduction / response to ethanol / transcription coactivator activity / cell surface receptor signaling pathway / response to hypoxia / Ub-specific processing proteases / regulation of cell cycle / apoptotic process / protein-containing complex binding / negative regulation of apoptotic process / zinc ion binding / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
BIRC2/BIRC3, UBA domain / : / BIRC2/3-like, UBA domain / Caspase recruitment domain / BIR repeat. / BIR repeat / Inhibitor of Apoptosis domain / BIR repeat profile. / Baculoviral inhibition of apoptosis protein repeat / CARD domain ...BIRC2/BIRC3, UBA domain / : / BIRC2/3-like, UBA domain / Caspase recruitment domain / BIR repeat. / BIR repeat / Inhibitor of Apoptosis domain / BIR repeat profile. / Baculoviral inhibition of apoptosis protein repeat / CARD domain / CARD caspase recruitment domain profile. / Caspase recruitment domain / Zinc finger, C3HC4 type (RING finger) / Death-like domain superfamily / Ring finger / Zinc finger RING-type profile. / Zinc finger, RING-type
Similarity search - Domain/homology
Chem-TKY / Baculoviral IAP repeat-containing protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.11 Å
AuthorsCalabrese, M.F. / Schiemer, J.S.
CitationJournal: Nat.Chem.Biol. / Year: 2020
Title: Structural Characterization of BTK:PROTAC:cIAP Ternary Complexes: From Snapshots to Ensembles
Authors: Calabrese, M.F. / Schiemer, J.S. / Horst, R. / Meng, Y. / Montgomery, J. / Xu, Y. / Feng, X. / Borzilleri, K. / Uccello, D.P. / Leverett, C. / Brown, S. / Che, Y. / Brown, M.F. / Hayward, M. ...Authors: Calabrese, M.F. / Schiemer, J.S. / Horst, R. / Meng, Y. / Montgomery, J. / Xu, Y. / Feng, X. / Borzilleri, K. / Uccello, D.P. / Leverett, C. / Brown, S. / Che, Y. / Brown, M.F. / Hayward, M.M. / Gilbert, A.M. / Noe, M.C.
History
DepositionMar 18, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 18, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Baculoviral IAP repeat-containing protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,5643
Polymers11,3191
Non-polymers1,2462
Water91951
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)49.037, 33.651, 57.610
Angle α, β, γ (deg.)90.000, 105.700, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Baculoviral IAP repeat-containing protein 2 / Cellular inhibitor of apoptosis 1 / C-IAP1 / IAP homolog B / Inhibitor of apoptosis protein 2 / ...Cellular inhibitor of apoptosis 1 / C-IAP1 / IAP homolog B / Inhibitor of apoptosis protein 2 / hIAP2 / RING finger protein 48 / RING-type E3 ubiquitin transferase BIRC2 / TNFR2-TRAF-signaling complex protein 2


Mass: 11318.731 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BIRC2, API1, MIHB, RNF48 / Production host: Escherichia coli (E. coli)
References: UniProt: Q13490, RING-type E3 ubiquitin transferase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-TKY / 14-{[(3S)-2-(N-methyl-L-alanyl-3-methyl-L-valyl)-3-{[(1R)-1,2,3,4-tetrahydronaphthalen-1-yl]carbamoyl}-1,2,3,4-tetrahydroisoquinolin-7-yl]oxy}-3,6,9,12-tetraoxatetradecan-1-yl (3R)-3-{5-amino-4-carbamoyl-3-[4-(2,4-difluorophenoxy)phenyl]-1H-pyrazol-1-yl}piperidine-1-carboxylate


Mass: 1180.341 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C62H79F2N9O12 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 51 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.02 Å3/Da / Density % sol: 39.15 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 0.2M Magnesium Acetate Tetrahydrate, 20% w/v PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.99988 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 3, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99988 Å / Relative weight: 1
ReflectionResolution: 2.1→27.4 Å / Num. obs: 4750 / % possible obs: 88.6 % / Redundancy: 3.3 % / Biso Wilson estimate: 34.15 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.07 / Net I/σ(I): 9.9
Reflection shellResolution: 2.107→2.116 Å / Rmerge(I) obs: 0.418 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 63 / CC1/2: 0.96

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Processing

Software
NameVersionClassification
XDSdata reduction
BUSTER2.11.7refinement
PDB_EXTRACT3.25data extraction
autoPROCdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4kmn

4kmn


Resolution: 2.11→27.4 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.896 / SU R Cruickshank DPI: 0.281 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.306 / SU Rfree Blow DPI: 0.232 / SU Rfree Cruickshank DPI: 0.228
RfactorNum. reflection% reflectionSelection details
Rfree0.258 244 5.14 %RANDOM
Rwork0.187 ---
obs0.191 4746 88.6 %-
Displacement parametersBiso max: 90.23 Å2 / Biso mean: 43.34 Å2 / Biso min: 23.05 Å2
Baniso -1Baniso -2Baniso -3
1--5.0515 Å20 Å2-8.0202 Å2
2---1.8921 Å20 Å2
3---6.9435 Å2
Refine analyzeLuzzati coordinate error obs: 0.29 Å
Refinement stepCycle: final / Resolution: 2.11→27.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms684 0 40 51 775
Biso mean--56.82 49.16 -
Num. residues----87
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d246SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes143HARMONIC5
X-RAY DIFFRACTIONt_it750HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion88SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact899SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d750HARMONIC20.007
X-RAY DIFFRACTIONt_angle_deg1023HARMONIC20.86
X-RAY DIFFRACTIONt_omega_torsion2.25
X-RAY DIFFRACTIONt_other_torsion15.49
LS refinement shellResolution: 2.11→2.16 Å / Rfactor Rfree error: 0 / Total num. of bins used: 12
RfactorNum. reflection% reflection
Rfree0.2817 19 4.8 %
Rwork0.2157 377 -
all0.2191 396 -
obs--98.76 %
Refinement TLS params.Method: refined / Origin x: 58.2869 Å / Origin y: 5.6017 Å / Origin z: 12.7624 Å
111213212223313233
T-0.0312 Å20.0386 Å20.0323 Å2--0.0368 Å2-0.0191 Å2---0.1063 Å2
L2.1012 °20.0646 °2-0.2537 °2-4.1368 °20.8083 °2--5.2274 °2
S-0.1031 Å °-0.216 Å °0.0968 Å °0.5387 Å °0.0992 Å °0.0883 Å °0.1065 Å °0.2403 Å °0.0038 Å °
Refinement TLS groupSelection details: { A|* }

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