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- PDB-9n1r: Crystal structure of XIAP-BIR3 with ALP2 series SMAC mimetic ligand -

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Basic information

Entry
Database: PDB / ID: 9n1r
TitleCrystal structure of XIAP-BIR3 with ALP2 series SMAC mimetic ligand
ComponentsE3 ubiquitin-protein ligase XIAP
KeywordsSIGNALING PROTEIN / TRANSFERASE / 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: 2.8 Å
AuthorsNguyen, S. / Lucet, I. / Roy, M.J.
Funding support Australia, 2items
OrganizationGrant numberCountry
Other private
National Health and Medical Research Council (NHMRC, Australia)GNT9000719, 1107149, 1195038 Australia
Citation
Journal: 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.
#1: Journal: Acta Crystallogr D Struct Biol / Year: 2019
Title: Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix.
Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty ...Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty / Robert D Oeffner / Billy K Poon / Michael G Prisant / Randy J Read / Jane S Richardson / David C Richardson / Massimo D Sammito / Oleg V Sobolev / Duncan H Stockwell / Thomas C Terwilliger / Alexandre G Urzhumtsev / Lizbeth L Videau / Christopher J Williams / Paul D Adams /
Abstract: Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological ...Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological processes and to develop new therapeutics against diseases. The overall structure-solution workflow is similar for these techniques, but nuances exist because the properties of the reduced experimental data are different. Software tools for structure determination should therefore be tailored for each method. Phenix is a comprehensive software package for macromolecular structure determination that handles data from any of these techniques. Tasks performed with Phenix include data-quality assessment, map improvement, model building, the validation/rebuilding/refinement cycle and deposition. Each tool caters to the type of experimental data. The design of Phenix emphasizes the automation of procedures, where possible, to minimize repetitive and time-consuming manual tasks, while default parameters are chosen to encourage best practice. A graphical user interface provides access to many command-line features of Phenix and streamlines the transition between programs, project tracking and re-running of previous tasks.
#2: Journal: J Synchrotron Radiat / Year: 2002
Title: Blu-Ice and the Distributed Control System: software for data acquisition and instrument control at macromolecular crystallography beamlines.
Authors: McPhillips, T.M. / McPhillips, S.E. / Chiu, H.J. / Cohen, A.E. / Deacon, A.M. / Ellis, P.J. / Garman, E. / Gonzalez, A. / Sauter, N.K. / Phizackerley, R.P. / Soltis, S.M. / Kuhn, P.
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.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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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
B: E3 ubiquitin-protein ligase XIAP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,2706
Polymers25,3782
Non-polymers8924
Water19811
1
A: E3 ubiquitin-protein ligase XIAP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,1353
Polymers12,6891
Non-polymers4462
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: E3 ubiquitin-protein ligase XIAP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,1353
Polymers12,6891
Non-polymers4462
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)99.710, 99.710, 105.430
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Space group name HallP4abw2nw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+1/4
#3: y+1/2,-x+1/2,z+3/4
#4: x+1/2,-y+1/2,-z+3/4
#5: -x+1/2,y+1/2,-z+1/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 248 through 336 or (resid 337...
d_2ens_1chain "B"

NCS domain segments:

Component-ID: 1 / Ens-ID: ens_1 / Beg auth comp-ID: ARG / Beg label comp-ID: ARG / End auth comp-ID: LEU / End label comp-ID: LEU / Auth seq-ID: 248 - 352 / Label seq-ID: 4 - 108

Dom-IDAuth asym-IDLabel asym-ID
d_1AA
d_2BB

NCS oper: (Code: givenMatrix: (-0.99581688624, 0.0913654769007, -0.00103860926519), (0.0909779214322, 0.992518434659, 0.0814258845479), (0.00847035361589, 0.0809907802977, -0.996678858317)Vector: 3. ...NCS oper: (Code: given
Matrix: (-0.99581688624, 0.0913654769007, -0.00103860926519), (0.0909779214322, 0.992518434659, 0.0814258845479), (0.00847035361589, 0.0809907802977, -0.996678858317)
Vector: 3.45762227059, -1.38317599134, 27.0399154899)

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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.: 2 / Fragment: residues 246-354
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.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-A1BUO / N-{(5M)-5-(3,5-dimethyl-1H-pyrazol-4-yl)-6-[(1,3-thiazol-5-yl)ethynyl]pyridin-2-yl}-N~2~-methyl-L-alaninamide


Mass: 380.467 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C19H20N6OS / 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: 5.16 Å3/Da / Density % sol: 76.18 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 0.05 - 0.2 M HEPES pH 8.0 and 3.0 - 3.4 M NaCl

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.953732 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 30, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.953732 Å / Relative weight: 1
ReflectionResolution: 2.8→45.07 Å / Num. obs: 20489 / % possible obs: 100 % / Redundancy: 26.4 % / Biso Wilson estimate: 75.35 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.268 / Net I/σ(I): 14.6
Reflection shellResolution: 2.8→3.02 Å / Redundancy: 27.3 % / Rmerge(I) obs: 5.356 / Mean I/σ(I) obs: 2 / Num. unique obs: 3205 / CC1/2: 0.799 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.21.1_5286refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→45.07 Å / SU ML: 0.3691 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 29.2633
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2111 659 4.85 %
Rwork0.2035 12930 -
obs0.2041 13589 99.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 80.78 Å2
Refinement stepCycle: LAST / Resolution: 2.8→45.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1694 0 56 11 1761
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00961808
X-RAY DIFFRACTIONf_angle_d1.13152456
X-RAY DIFFRACTIONf_chiral_restr0.0573234
X-RAY DIFFRACTIONf_plane_restr0.0086318
X-RAY DIFFRACTIONf_dihedral_angle_d22.2249626
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 0.649959858944 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8-3.020.34031090.34392554X-RAY DIFFRACTION99.59
3.02-3.320.25761150.25712539X-RAY DIFFRACTION99.74
3.32-3.80.24151110.21352574X-RAY DIFFRACTION99.89
3.8-4.790.20591300.17492590X-RAY DIFFRACTION99.67
4.79-45.070.18591940.1822673X-RAY DIFFRACTION99.51
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)
18.0390384862-0.1387386827161.110419879443.501639038220.4786257249098.09370261044-0.117912819370.0324244981466-0.269464031079-0.207228929540.1254510027660.09932253470620.4848402283030.8768662005220.01957528077070.5595365286030.124393841292-0.03790793854980.523547271562-0.0409392102320.56761323827515.9498835816-20.3029327954.61481629286
27.80435028722-1.184590620050.797658829912.33184823835-0.8015439316343.2360151424-0.2387236855750.04854273539010.136155170788-0.3330854593360.3245736103040.09109653166920.0562191901682-0.0657978123422-0.1334039990690.7683778401860.078782542439-0.03488221831080.552554380639-0.04279276697840.6182058395442.91603361571-14.80966532042.88042009705
36.914613690252.60317242936-4.68611157357.15715608221-0.6000858466957.09210434691-0.01141375599021.07574965750.1423879950660.201972048884-0.126320633881-0.06701760293430.451718859618-0.675887086146-0.01823120499150.634156695903-0.00855399272597-0.09321521846260.8049925871860.1828753153880.871592629898-12.1537438962-14.863314196910.8678245056
47.646349549441.84377143095-1.829898376776.19241211299-3.431754043477.10380839748-0.320202024675-0.843774747111-0.4087115227061.013197893930.1696126547140.2165719542310.478919960456-1.086965769980.1973279413050.643367384165-0.09933789205820.04925321141380.5206091912290.02122767283940.442440504858-16.0985893562-20.293624088826.7559643723
55.94017561101-1.443860781830.8277880062011.28952822907-2.234278707394.54386389929-0.8360935138030.435000475461-0.9423040058620.5760697909230.034444516685-1.237158949551.14847498237-0.8590219757460.8898033518291.02330536503-0.005207045597370.1098708471790.396410619452-0.02999232013330.940066353794-12.2667161938-26.669762993420.4097303266
68.771245127022.55701920225-1.829249228661.823876664271.411103014675.859774784930.0196071590413-0.0671747349689-0.00505682390970.176974403398-0.0316940926946-0.0748583291730.3316283605310.125148110698-0.1084693225960.8573391884740.01138259181130.003987738722360.4709083938540.06438455846520.646417022657-5.09238585589-16.488365634621.76503415
79.48292531899-0.8976906178472.013785595286.56039550559-2.691585400285.6263933268-0.333404918958-0.2336390824960.126577594351-0.8003210194560.891647773238-0.3461148728170.0133727210512-0.68828234076-0.6571641695330.836460025471-0.111778349536-0.09664621448650.759685910097-0.03871528977810.7820720436267.21622677275-13.881253716425.1346860642
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 249 through 300 )AA249 - 3002 - 53
22chain 'A' and (resid 301 through 353 )AA301 - 35354 - 106
33chain 'B' and (resid 249 through 264 )BB249 - 2642 - 17
44chain 'B' and (resid 265 through 291 )BB265 - 29118 - 44
55chain 'B' and (resid 292 through 300 )BB292 - 30045 - 53
66chain 'B' and (resid 301 through 335 )BB301 - 33554 - 88
77chain 'B' and (resid 336 through 352 )BB336 - 35289 - 105

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