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- PDB-4kmn: Structure of cIAP1-BIR3 and inhibitor -

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Basic information

Entry
Database: PDB / ID: 4kmn
TitleStructure of cIAP1-BIR3 and inhibitor
ComponentsBaculoviral IAP repeat-containing protein 2
KeywordsLIGASE/LIGASE INHIBITOR / apoptosis / cIAP1-BIR3 / LIGASE-LIGASE INHIBITOR complex
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 / XY body / negative regulation of necroptotic process / cysteine-type endopeptidase inhibitor activity involved in apoptotic process / non-canonical NF-kappaB signal transduction / TNFR1-induced proapoptotic signaling / positive regulation of protein monoubiquitination / RIPK1-mediated regulated necrosis / regulation of reactive oxygen species metabolic process / regulation of toll-like receptor signaling pathway / regulation of innate immune response / Apoptotic cleavage of cellular proteins / necroptotic process / regulation of cell differentiation / canonical NF-kappaB signal transduction / response to cAMP / tumor necrosis factor-mediated signaling pathway / placenta development / TICAM1, RIP1-mediated IKK complex recruitment / ubiquitin binding / IKK complex recruitment mediated by RIP1 / positive regulation of protein ubiquitination / 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 / regulation of apoptotic process / response to ethanol / proteasome-mediated ubiquitin-dependent protein catabolic process / response to hypoxia / transcription coactivator activity / positive regulation of canonical NF-kappaB signal transduction / cell surface receptor signaling pathway / 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 / Inhibitor Of Apoptosis Protein (2mihbC-IAP-1); Chain A / Inhibitor Of Apoptosis Protein (2mihbC-IAP-1); Chain A / : / Caspase recruitment domain / BIR repeat. / BIR repeat / Inhibitor of Apoptosis domain ...BIRC2/BIRC3, 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 / : / 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 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-436 / PHOSPHATE ION / Baculoviral IAP repeat-containing protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.523 Å
AuthorsLi, X. / Wang, J. / Condon, S.M. / Shi, Y.
CitationJournal: To be Published
Title: Structure of cIAP1-BIR3 and inhibitor
Authors: Li, X. / Wang, J. / Condon, S.M. / Shi, Y.
History
DepositionMay 8, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 14, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / 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_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_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 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,7904
Polymers11,8221
Non-polymers9673
Water2,162120
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)67.714, 67.714, 66.913
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Baculoviral IAP repeat-containing protein 2 / C-IAP1 / IAP homolog B / Inhibitor of apoptosis protein 2 / IAP-2 / hIAP-2 / hIAP2 / RING finger ...C-IAP1 / IAP homolog B / Inhibitor of apoptosis protein 2 / IAP-2 / hIAP-2 / hIAP2 / RING finger protein 48 / TNFR2-TRAF-signaling complex protein 2


Mass: 11822.384 Da / Num. of mol.: 1 / Fragment: UNP residues 260-357
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BIRC2, API1, IAP2, MIHB, RNF48 / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q13490, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases)
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-436 / (2S)-N-{(2R)-1-[(2R,4S)-2-{[6,6'-difluoro-3'-({(2R,4S)-4-hydroxy-1-[(2S)-2-{[(2S)-2-(methylamino)propanoyl]amino}butanoyl]pyrrolidin-2-yl}methyl)-1H,1'H-2,2'-biindol-3-yl]methyl}-4-hydroxypyrrolidin-1-yl]-1-oxobutan-2-yl}-2-(methylamino)propanamide


Mass: 806.941 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C42H56F2N8O6
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 120 / Source method: isolated from a natural source / Formula: H2O

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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: 3.75 Å3/Da / Density % sol: 67.16 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.9
Details: 1M Na/K phosphate pH6.9, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Jan 31, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.52→30.21 Å / Num. obs: 26150

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Processing

SoftwareName: PHENIX / Version: (phenix.refine: 1.5_2) / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1G73

1g73


Resolution: 1.523→30.21 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8701 / SU ML: 0.15 / σ(F): 1.36 / Phase error: 19.38 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1991 1321 5.07 %
Rwork0.1595 --
obs0.1613 26069 94.48 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 60.162 Å2 / ksol: 0.457 e/Å3
Displacement parametersBiso max: 78.46 Å2 / Biso mean: 35.0843 Å2 / Biso min: 17.64 Å2
Baniso -1Baniso -2Baniso -3
1-2.0985 Å20 Å2-0 Å2
2--2.0985 Å20 Å2
3----4.1971 Å2
Refinement stepCycle: LAST / Resolution: 1.523→30.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms828 0 64 120 1012
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01921
X-RAY DIFFRACTIONf_angle_d1.5581255
X-RAY DIFFRACTIONf_dihedral_angle_d18.328327
X-RAY DIFFRACTIONf_chiral_restr0.069121
X-RAY DIFFRACTIONf_plane_restr0.007160
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.5228-1.58380.3121960.2666183164
1.5838-1.65590.30881680.234256491
1.6559-1.74310.20921590.18285499
1.7431-1.85230.18411480.14122867100
1.8523-1.99530.16441510.13142893100
1.9953-2.19610.16051540.12442898100
2.1961-2.51370.17481530.12672922100
2.5137-3.16650.2021480.13952941100
3.1665-30.21590.19981440.1776297897

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