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- PDB-9n21: Crystal structure of XIAP-BIR3 with ALP1 series SMAC mimetic ligand -

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Basic information

Entry
Database: PDB / ID: 9n21
TitleCrystal structure of XIAP-BIR3 with ALP1 series SMAC mimetic ligand
ComponentsE3 ubiquitin-protein ligase XIAP
KeywordsSIGNALING PROTEIN / Ubiquitin E3 ligase / Inhibitor of Apoptosis Protein / Cell death / SMAC mimetic.
Function / homology
Function and homology information


regulation of apoptosis involved in tissue homeostasis / positive regulation of protein linear polyubiquitination / copper ion homeostasis / regulation of BMP signaling pathway / regulation of nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway / nucleotide-binding oligomerization domain containing 1 signaling pathway / nucleotide-binding oligomerization domain containing 2 signaling pathway / SMAC, XIAP-regulated apoptotic response / Activation of caspases through apoptosome-mediated cleavage / cysteine-type endopeptidase inhibitor activity involved in apoptotic process ...regulation of apoptosis involved in tissue homeostasis / positive regulation of protein linear polyubiquitination / copper ion homeostasis / regulation of BMP signaling pathway / regulation of nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway / nucleotide-binding oligomerization domain containing 1 signaling pathway / nucleotide-binding oligomerization domain containing 2 signaling pathway / SMAC, XIAP-regulated apoptotic response / Activation of caspases through apoptosome-mediated cleavage / cysteine-type endopeptidase inhibitor activity involved in apoptotic process / Regulation of the apoptosome activity / 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 / positive regulation of type I interferon production / protein K63-linked ubiquitination / cysteine-type endopeptidase inhibitor activity / negative regulation of tumor necrosis factor-mediated signaling pathway / protein serine/threonine kinase binding / Regulation of PTEN localization / positive regulation of protein ubiquitination / TNFR1-induced NF-kappa-B signaling pathway / Deactivation of the beta-catenin transactivating complex / Regulation of TNFR1 signaling / RING-type E3 ubiquitin transferase / positive regulation of JNK cascade / Regulation of necroptotic cell death / Regulation of PTEN stability and activity / Wnt signaling pathway / ubiquitin-protein transferase activity / ubiquitin protein ligase activity / positive regulation of canonical Wnt signaling pathway / regulation of inflammatory response / neuron apoptotic process / regulation of apoptotic process / response to lipopolysaccharide / positive regulation of canonical NF-kappaB signal transduction / regulation of cell cycle / defense response to bacterium / DNA damage response / negative regulation of apoptotic process / zinc ion binding / nucleoplasm / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
XIAP/BIRC8, UBA domain / : / BIRC2/3-like, UBA domain / : / BIR repeat. / BIR repeat / Inhibitor of Apoptosis domain / BIR repeat profile. / Baculoviral inhibition of apoptosis protein repeat / Zinc finger, C3HC4 type (RING finger) ...XIAP/BIRC8, UBA domain / : / BIRC2/3-like, UBA domain / : / 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
Similarity search - Domain/homology
: / E3 ubiquitin-protein ligase XIAP
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.74 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: E3 ubiquitin-protein ligase XIAP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,0413
Polymers12,6891
Non-polymers3522
Water19811
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, Purified protein elutes as a monomer, surface plasmon resonance, Small molecule binding to purified protein fits 1:1 binding model
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area6190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.235, 71.235, 105.550
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number91
Space group name H-MP4122
Space group name HallP4w2c
Symmetry operation#1: x,y,z
#2: -y,x,z+1/4
#3: y,-x,z+3/4
#4: x,-y,-z+1/2
#5: -x,y,-z
#6: -x,-y,z+1/2
#7: y,x,-z+3/4
#8: -y,-x,-z+1/4

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Components

#1: Protein E3 ubiquitin-protein ligase XIAP / Baculoviral IAP repeat-containing protein 4 / IAP-like protein / ILP / hILP / Inhibitor of ...Baculoviral IAP repeat-containing protein 4 / IAP-like protein / ILP / hILP / Inhibitor of apoptosis protein 3 / IAP-3 / hIAP-3 / hIAP3 / RING-type E3 ubiquitin transferase XIAP / X-linked inhibitor of apoptosis protein / X-linked IAP


Mass: 12689.146 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: XIAP, API3, BIRC4, IAP3 / Production host: Escherichia coli (E. coli)
References: UniProt: P98170, 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-A1BVB / N~2~-methyl-N-{6-[(1,3-thiazol-5-yl)ethynyl]pyridin-2-yl}-L-alaninamide


Mass: 286.352 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H14N4OS / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 11 / 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: 5.28 Å3/Da / Density % sol: 76.69 %
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: Feb 16, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.74→45.46 Å / Num. obs: 7616 / % possible obs: 99.6 % / Redundancy: 25.4 % / Biso Wilson estimate: 72.23 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.13 / Rpim(I) all: 0.026 / Rrim(I) all: 0.133 / Χ2: 0.51 / Net I/σ(I): 16.5 / Num. measured all: 193363
Reflection shellResolution: 2.74→2.87 Å / % possible obs: 97.4 % / Redundancy: 24.1 % / Rmerge(I) obs: 1.516 / Num. measured all: 22972 / Num. unique obs: 952 / CC1/2: 0.846 / Rpim(I) all: 0.309 / Rrim(I) all: 1.548 / Χ2: 0.41 / Net I/σ(I) obs: 2

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Processing

Software
NameVersionClassificationNB
PHENIX1.21.1_5286refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.74→42.41 Å / SU ML: 0.4014 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.9262
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2191 359 4.74 %
Rwork0.2015 7212 -
obs0.2023 7571 99.42 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 75.61 Å2
Refinement stepCycle: LAST / Resolution: 2.74→42.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms839 0 21 11 871
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008888
X-RAY DIFFRACTIONf_angle_d1.02961203
X-RAY DIFFRACTIONf_chiral_restr0.0497114
X-RAY DIFFRACTIONf_plane_restr0.0067157
X-RAY DIFFRACTIONf_dihedral_angle_d24.6917311
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.74-3.140.37571100.29892314X-RAY DIFFRACTION98.42
3.14-3.950.27191190.23182384X-RAY DIFFRACTION99.88
3.95-42.410.16611300.16912514X-RAY DIFFRACTION99.92
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
19.246523778553.264882238594.752275973922.829627492940.3572866411018.933339394470.542787102415-0.794972794035-0.2387870499450.138360696089-0.5675100790670.1103299469291.00678279949-0.5030171562820.1211554623630.734841453448-0.0773137720860.01134634415350.7498054876190.09137790849130.77864205001812.5271119396-35.414412840710.9819616625
23.01554578233-1.875299400292.902329158434.22188238466-1.424826969953.001548989720.05983224089761.038558751930.695869980838-0.949612281892-0.184810074007-0.1594521125360.531227713398-0.01497600017470.2507813278930.795653760.049109700864-0.06032103702010.9441830517030.0970072445240.5763885364799.46536313986-30.9464021125-1.94124701007
37.221047664211.702456271552.106410781777.44881966375-1.507742871766.66011677645-0.008122617011040.3144661954711.081957785550.176440883708-0.5622002736240.225769349819-0.8426563104120.2569320833660.6005890204190.7203430276790.05115265945560.03825176061030.7925770649940.06013967479980.69120714716912.277070985-25.4053575433.38627921393
46.394092587493.191921102171.364940458972.070737125791.251729325174.94429672812-0.2445504256591.176345146381.12420658585-0.3547964314940.3575650895380.662725380415-0.2429405776010.187663940672-0.1175830188230.6328477460880.166312739896-0.03378919523390.8450824067610.1485162934820.59596246295221.2584140582-25.96757929822.68268925188
56.126496118942.771443257780.08230546348945.238656499863.836247983517.096365102640.248168620589-0.369466576232-0.6301484370690.00633221701325-0.238572591607-0.1557617007880.3279006022880.39296285430.01152590932950.6477615634320.103725781623-0.01276762303830.759687955780.1038609673830.80256811039423.6105721441-33.43142221338.07320056625
69.1302650134-0.261669122845-0.8933230469196.73582362860.1541970563156.502474394050.511229619554-0.8141898706340.198003841233-0.2319335257980.0915780769299-0.3411586472351.0299131438-0.680046807465-0.3858148137390.733704870836-0.102184332728-0.0161148933820.9305951514160.09551219235170.73601048760430.7872161177-23.1003056761.48501318661
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid 249 through 271 )249 - 2711 - 23
22chain 'A' and (resid 272 through 291 )272 - 29124 - 43
33chain 'A' and (resid 292 through 315 )292 - 31544 - 67
44chain 'A' and (resid 316 through 323 )316 - 32368 - 75
55chain 'A' and (resid 324 through 335 )324 - 33576 - 87
66chain 'A' and (resid 336 through 351 )336 - 35188 - 103

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