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- PDB-9n23: Crystal structure of cIAP1-BIR3 with XB2 series SMAC mimetic ligand -

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Basic information

Entry
Database: PDB / ID: 9n23
TitleCrystal structure of cIAP1-BIR3 with XB2 series SMAC mimetic ligand
ComponentsBaculoviral IAP repeat-containing protein 2
KeywordsSIGNALING PROTEIN / Ubiquitin E3 ligase / Inhibitor of Apoptosis Protein / Cell death / SMAC mimetic.
Function / homology
Function and homology information


negative regulation of ripoptosome assembly involved in necroptotic process / 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 ...negative regulation of ripoptosome assembly involved in necroptotic process / 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 / negative regulation of necroptotic process / XY body / cysteine-type endopeptidase inhibitor activity involved in apoptotic process / non-canonical NF-kappaB signal transduction / positive regulation of protein monoubiquitination / TNFR1-induced proapoptotic signaling / regulation of reactive oxygen species metabolic process / RIPK1-mediated regulated necrosis / regulation of toll-like receptor signaling pathway / Apoptotic cleavage of cellular proteins / regulation of innate immune response / necroptotic process / regulation of cell differentiation / canonical NF-kappaB signal transduction / response to cAMP / placenta development / ubiquitin binding / TICAM1, RIP1-mediated IKK complex recruitment / positive regulation of protein ubiquitination / tumor necrosis factor-mediated signaling pathway / IKK complex recruitment mediated by RIP1 / TNFR1-induced NF-kappa-B signaling pathway / TNFR2 non-canonical NF-kB pathway / Regulation of TNFR1 signaling / NOD1/2 Signaling Pathway / RING-type E3 ubiquitin transferase / 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 / transferase activity / regulation of inflammatory response / response to ethanol / regulation of apoptotic process / proteasome-mediated ubiquitin-dependent protein catabolic process / response to hypoxia / transcription coactivator activity / cell surface receptor signaling pathway / positive regulation of canonical NF-kappaB signal transduction / regulation of cell cycle / Ub-specific processing proteases / apoptotic process / negative regulation of apoptotic process / protein-containing complex binding / zinc ion binding / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
BIRC2/BIRC3, UBA domain / : / BIRC2/3-like, UBA domain / : / BIR repeat. / Caspase recruitment domain / BIR repeat / Inhibitor of Apoptosis domain / BIR repeat profile. / Baculoviral inhibition of apoptosis protein repeat ...BIRC2/BIRC3, UBA domain / : / BIRC2/3-like, UBA domain / : / BIR repeat. / Caspase recruitment domain / 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
: / Baculoviral IAP repeat-containing protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsNguyen, S. / Lucet, I. / Roy, M.J.
Funding support Australia, 3items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia)GNT9000719 Australia
National Health and Medical Research Council (NHMRC, Australia)GNT1107149 Australia
National Health and Medical Research Council (NHMRC, Australia)GNT1195038 Australia
CitationJournal: Commun Chem / Year: 2026
Title: Expanding the toolbox to develop IAP-based degraders of TEAD transcription factors.
Authors: Gupta, N. / Trainor, N. / Radwan, M. / Nguyen, S. / Duncan, L. / Tang, A.X. / Beveridge, J. / Silke, N. / Yousef, J. / Bilgilier, C. / Wachter, J. / Greb, P. / Jandova, Z. / Elias, J. / ...Authors: Gupta, N. / Trainor, N. / Radwan, M. / Nguyen, S. / Duncan, L. / Tang, A.X. / Beveridge, J. / Silke, N. / Yousef, J. / Bilgilier, C. / Wachter, J. / Greb, P. / Jandova, Z. / Elias, J. / Kopf, S. / Gerstberger, T. / Stolt-Bergner, P. / Braun, N. / Weinstabl, H. / McConnell, D.B. / Mauri, F. / Lucet, I.S. / Silke, J. / Chessum, N.E.A. / Roy, M.J.
History
DepositionJan 27, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 21, 2026Provider: repository / Type: Initial release
Revision 1.1Feb 4, 2026Group: Database references / Category: citation / citation_author / Item: _citation.pdbx_database_id_PubMed / _citation.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)23,0456
Polymers22,0412
Non-polymers1,0044
Water1,60389
1
A: Baculoviral IAP repeat-containing protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,5223
Polymers11,0201
Non-polymers5022
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Baculoviral IAP repeat-containing protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,5223
Polymers11,0201
Non-polymers5022
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)30.252, 68.386, 124.224
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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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 / hIAP-2 / hIAP2 / RING finger protein 48 / RING-type E3 ubiquitin transferase BIRC2 / TNFR2-TRAF-signaling complex protein 2


Mass: 11020.435 Da / Num. of mol.: 2
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.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-A1BVC / N-methyl-L-alanyl-3-methyl-L-valyl-N-(2-fluoro-5-methoxyphenyl)-L-prolinamide


Mass: 436.520 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C22H33FN4O4 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 89 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.91 Å3/Da / Density % sol: 57.8 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.05-0.2 M HEPES, pH 8.0, 3.0-3.4 M sodium chloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 3, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.8→41.41 Å / Num. obs: 24833 / % possible obs: 100 % / Redundancy: 13.2 % / Biso Wilson estimate: 23.18 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.327 / Rpim(I) all: 0.093 / Rrim(I) all: 0.34 / Χ2: 0.96 / Net I/σ(I): 9
Reflection shellResolution: 1.8→1.84 Å / Redundancy: 13.2 % / Rmerge(I) obs: 5.52 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 1423 / CC1/2: 0.512 / Rpim(I) all: 1.571 / Rrim(I) all: 5.742 / Χ2: 0.88 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.21.1_5286refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→35.42 Å / SU ML: 0.228 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.5449
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2223 1256 5.07 %
Rwork0.1931 23502 -
obs0.1946 24758 99.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 26.98 Å2
Refinement stepCycle: LAST / Resolution: 1.8→35.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1505 0 64 89 1658
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00661655
X-RAY DIFFRACTIONf_angle_d1.04232251
X-RAY DIFFRACTIONf_chiral_restr0.0544209
X-RAY DIFFRACTIONf_plane_restr0.0081297
X-RAY DIFFRACTIONf_dihedral_angle_d19.8644589
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.870.29411440.27522551X-RAY DIFFRACTION99.85
1.87-1.960.27731360.2622549X-RAY DIFFRACTION99.89
1.96-2.060.28631390.2332571X-RAY DIFFRACTION99.96
2.06-2.190.26461520.20782566X-RAY DIFFRACTION100
2.19-2.360.21171240.18972592X-RAY DIFFRACTION99.93
2.36-2.60.25091200.20552609X-RAY DIFFRACTION99.85
2.6-2.970.26141480.21322624X-RAY DIFFRACTION100
2.97-3.740.2341240.18262670X-RAY DIFFRACTION99.96
3.74-35.420.16551690.15662770X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 6.78952429495 Å / Origin y: 22.5348159461 Å / Origin z: 38.1784610238 Å
111213212223313233
T0.139332351143 Å20.00601631648777 Å20.0142288814734 Å2-0.178239574217 Å20.0303690523674 Å2--0.265407125226 Å2
L1.01508884186 °20.339542720466 °20.649475912429 °2-0.861180643295 °20.781640203382 °2--1.85156169039 °2
S-0.0373902391129 Å °0.0209890359034 Å °-0.0392413703937 Å °-0.0637132254625 Å °-0.0519733739834 Å °0.0369434067339 Å °0.000897119056518 Å °-0.0244333821341 Å °0.0941468653617 Å °
Refinement TLS groupSelection details: all

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