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- PDB-4mti: Crystal structure of cIAP1 BIR3 bound to T3258042 -

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Basic information

Entry
Database: PDB / ID: 4mti
TitleCrystal structure of cIAP1 BIR3 bound to T3258042
ComponentsBaculoviral IAP repeat-containing protein 2
KeywordsAPOPTOSIS INHIBITOR / RING-type zinc finger / Ligase
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 / positive regulation of protein K63-linked ubiquitination / regulation of necroptotic process / regulation of nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway ...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 / positive regulation of protein K63-linked ubiquitination / regulation of necroptotic process / regulation of nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway / CD40 receptor complex / XY body / negative regulation of necroptotic process / positive regulation of protein monoubiquitination / regulation of reactive oxygen species metabolic process / TNFR1-induced proapoptotic signaling / non-canonical NF-kappaB signal transduction / RIPK1-mediated regulated necrosis / regulation of toll-like receptor signaling pathway / regulation of cell differentiation / regulation of innate immune response / Apoptotic cleavage of cellular proteins / necroptotic process / cysteine-type endopeptidase inhibitor activity involved in apoptotic process / canonical NF-kappaB signal transduction / tumor necrosis factor-mediated signaling pathway / response to cAMP / TICAM1, RIP1-mediated IKK complex recruitment / IKK complex recruitment mediated by RIP1 / positive regulation of protein ubiquitination / ubiquitin binding / 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 / placenta development / Regulation of necroptotic cell death / cytoplasmic side of plasma membrane / protein polyubiquitination / ubiquitin-protein transferase activity / ubiquitin protein ligase activity / protein-folding chaperone binding / regulation of cell population proliferation / regulation of inflammatory response / transferase activity / regulation of apoptotic process / positive regulation of canonical NF-kappaB signal transduction / proteasome-mediated ubiquitin-dependent protein catabolic process / response to ethanol / transcription coactivator activity / cell surface receptor signaling pathway / regulation of cell cycle / response to hypoxia / Ub-specific processing proteases / protein-containing complex binding / negative regulation of apoptotic process / apoptotic process / zinc ion binding / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
BIRC2/BIRC3, UBA domain / Caspase recruitment domain / : / BIRC2/3-like, UBA domain / Inhibitor Of Apoptosis Protein (2mihbC-IAP-1); Chain A / Inhibitor Of Apoptosis Protein (2mihbC-IAP-1); Chain A / : / BIR repeat. / BIR repeat / Inhibitor of Apoptosis domain ...BIRC2/BIRC3, UBA domain / Caspase recruitment domain / : / BIRC2/3-like, UBA domain / Inhibitor Of Apoptosis Protein (2mihbC-IAP-1); Chain A / Inhibitor Of Apoptosis Protein (2mihbC-IAP-1); Chain A / : / 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-2DX / Baculoviral IAP repeat-containing protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsSnell, G.P. / Dougan, D.R.
CitationJournal: Bioorg.Med.Chem. / Year: 2013
Title: Design, synthesis, and biological activities of novel hexahydropyrazino[1,2-a]indole derivatives as potent inhibitors of apoptosis (IAP) proteins antagonists with improved membrane ...Title: Design, synthesis, and biological activities of novel hexahydropyrazino[1,2-a]indole derivatives as potent inhibitors of apoptosis (IAP) proteins antagonists with improved membrane permeability across MDR1 expressing cells.
Authors: Shiokawa, Z. / Hashimoto, K. / Saito, B. / Oguro, Y. / Sumi, H. / Yabuki, M. / Yoshimatsu, M. / Kosugi, Y. / Debori, Y. / Morishita, N. / Dougan, D.R. / Snell, G.P. / Yoshida, S. / Ishikawa, T.
History
DepositionSep 19, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 11, 2013Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_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_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_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
B: Baculoviral IAP repeat-containing protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,8006
Polymers26,5902
Non-polymers1,2104
Water2,234124
1
A: Baculoviral IAP repeat-containing protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,9003
Polymers13,2951
Non-polymers6052
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Baculoviral IAP repeat-containing protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,9003
Polymers13,2951
Non-polymers6052
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)31.137, 68.476, 122.373
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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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: 13294.829 Da / Num. of mol.: 2 / Fragment: Bir3 (UNP Residues 260-352)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: API1, BIRC2, IAP2, MIHB, RNF48 / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BI21(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.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-2DX / (3S,8aR)-2-[(2S)-2-cyclohexyl-2-{[(2S)-2-(methylamino)butanoyl]amino}acetyl]-N-[(4R)-3,4-dihydro-2H-chromen-4-yl]octahydropyrrolo[1,2-a]pyrazine-3-carboxamide


Mass: 539.709 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C30H45N5O4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 124 / 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: 2.45 Å3/Da / Density % sol: 49.86 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.2
Details: 2.8M Na Cl, 0.06M Tris_base, 0.04M Tris Cl, pH 8.2, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.3 / Wavelength: 0.976 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 23, 2010
RadiationMonochromator: single-crystal Si(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 2.15→50 Å / Num. obs: 14267 / % possible obs: 95.2 % / Observed criterion σ(I): -3 / Redundancy: 4.3 % / Rmerge(I) obs: 0.15 / Net I/σ(I): 7
Reflection shellResolution: 2.15→2.19 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.55 / Num. unique all: 669 / % possible all: 92

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Processing

Software
NameVersionClassification
BOSdata collection
PHASERphasing
REFMAC5.6.0117refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.15→50 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.869 / SU B: 9.369 / SU ML: 0.136 / Cross valid method: THROUGHOUT / ESU R: 0.223 / ESU R Free: 0.213 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26713 724 5.1 %RANDOM
Rwork0.19461 ---
obs0.1982 13442 94.72 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.769 Å2
Baniso -1Baniso -2Baniso -3
1--2.17 Å20 Å2-0 Å2
2---3.22 Å2-0 Å2
3---5.39 Å2
Refinement stepCycle: LAST / Resolution: 2.15→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1508 0 80 124 1712
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0191660
X-RAY DIFFRACTIONr_bond_other_d0.0010.021128
X-RAY DIFFRACTIONr_angle_refined_deg1.2351.9732246
X-RAY DIFFRACTIONr_angle_other_deg0.89532692
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.7275182
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.29322.588
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.16515253
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.3081517
X-RAY DIFFRACTIONr_chiral_restr0.070.2214
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0211825
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02388
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.149→2.205 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.27 45 -
Rwork0.236 815 -
obs--87.13 %
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)
11.67030.64971.35453.98471.90753.7826-0.12610.07720.1162-0.25090.03180.1046-0.1277-0.0380.09430.04590.0026-0.05320.0351-0.01060.09910.188617.938126.3933
22.18960.0509-0.36.5433-4.06695.354-0.0229-0.2147-0.17090.2254-0.2661-0.1274-0.22610.33160.2890.0242-0.0244-0.03690.13260.05740.089113.356627.656248.8844
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A255 - 346
2X-RAY DIFFRACTION2B257 - 346

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