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- PDB-4lge: Crystal structure of clAP1 BIR3 bound to T3261256 -

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Basic information

Entry
Database: PDB / ID: 4lge
TitleCrystal structure of clAP1 BIR3 bound to T3261256
ComponentsBaculoviral IAP repeat-containing protein 2
KeywordsLigase/Ligase inhibitor / lAP family / 3 BIR repeats / 1 CARD domain / 1 RING-type zinc finger / Ligase-Ligase inhibitor complex
Function / homology
Function and homology information


negative regulation of ripoptosome assembly involved in necroptotic process / FBXO family protein binding / positive regulation of protein monoubiquitination / 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 / positive regulation of protein K63-linked ubiquitination / regulation of nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway ...negative regulation of ripoptosome assembly involved in necroptotic process / FBXO family protein binding / positive regulation of protein monoubiquitination / 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 / positive regulation of protein K63-linked ubiquitination / regulation of nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway / 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 / regulation of reactive oxygen species metabolic process / RIPK1-mediated regulated necrosis / regulation of toll-like receptor signaling pathway / regulation of innate immune response / Apoptotic cleavage of cellular proteins / necroptotic process / regulation of cell differentiation / response to cAMP / canonical NF-kappaB signal transduction / TICAM1, RIP1-mediated IKK complex recruitment / positive regulation of protein ubiquitination / IKK complex recruitment mediated by RIP1 / TNFR1-induced NF-kappa-B signaling pathway / TNFR2 non-canonical NF-kB pathway / placenta development / Regulation of TNFR1 signaling / ubiquitin binding / tumor necrosis factor-mediated signaling pathway / NOD1/2 Signaling Pathway / Regulation of necroptotic cell death / RING-type E3 ubiquitin transferase / 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 / transcription coactivator activity / response to hypoxia / cell surface receptor signaling pathway / positive regulation of canonical NF-kappaB signal transduction / Ub-specific processing proteases / regulation of cell cycle / 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
(4S,6aR,7aS)-5-{(2S)-2-cyclohexyl-2-[(N-methyl-L-alanyl)amino]acetyl}-N-[(4R)-3,4-dihydro-2H-chromen-4-yl]octahydro-1H-cyclopropa[4,5]pyrrolo[1,2-a]pyrazine-4-carboxamide / Chem-1Y0 / Baculoviral IAP repeat-containing protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å
AuthorsDougan, D.R.
CitationJournal: Bioorg.Med.Chem. / Year: 2013
Title: Design, stereoselective synthesis, and biological evaluation of novel tri-cyclic compounds as inhibitor of apoptosis proteins (IAP) antagonists.
Authors: Asano, M. / Hashimoto, K. / Saito, B. / Shiokawa, Z. / Sumi, H. / Yabuki, M. / Yoshimatsu, M. / Aoyama, K. / Hamada, T. / Morishita, N. / Dougan, D.R. / Mol, C.D. / Yoshida, S. / Ishikawa, T.
History
DepositionJun 27, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 28, 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_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_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

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)27,7966
Polymers26,5902
Non-polymers1,2064
Water4,071226
1
A: Baculoviral IAP repeat-containing protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,8983
Polymers13,2951
Non-polymers6032
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)13,8983
Polymers13,2951
Non-polymers6032
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)30.520, 72.805, 116.914
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: 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-1Y0 / (4S,6aR,7aS)-5-{(2S)-2-cyclohexyl-2-[(N-methyl-L-alanyl)amino]acetyl}-N-[(4R)-3,4-dihydro-2H-chromen-4-yl]octahydro-1H-cyclopropa[4,5]pyrrolo[1,2-a]pyrazine-4-carboxamide


Type: peptide-like, Peptide-like / Class: Antagonist / Mass: 537.694 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C30H43N5O4
References: (4S,6aR,7aS)-5-{(2S)-2-cyclohexyl-2-[(N-methyl-L-alanyl)amino]acetyl}-N-[(4R)-3,4-dihydro-2H-chromen-4-yl]octahydro-1H-cyclopropa[4,5]pyrrolo[1,2-a]pyrazine-4-carboxamide
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 226 / 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: 2.44 Å3/Da / Density % sol: 49.64 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 2.5M NaCl,1OOmM Tris,0.2M MgCl2, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.3
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 27, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 1.55→28.147 Å / Num. obs: 45061

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
REFMAC5.7.0025refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.55→28.147 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.963 / SU B: 2.124 / SU ML: 0.039 / Cross valid method: THROUGHOUT / ESU R: 0.066 / ESU R Free: 0.065 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.18199 1938 5.1 %RANDOM
Rwork0.16319 ---
obs0.16413 36291 98.45 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.608 Å2
Baniso -1Baniso -2Baniso -3
1--1.11 Å20 Å20 Å2
2---0.78 Å20 Å2
3---1.89 Å2
Refinement stepCycle: LAST / Resolution: 1.55→28.147 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1516 0 80 226 1822
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0191685
X-RAY DIFFRACTIONr_angle_refined_deg1.3211.9772287
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.3665185
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.89222.588
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.06915263
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.281517
X-RAY DIFFRACTIONr_chiral_restr0.090.2224
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0211321
LS refinement shellResolution: 1.55→1.59 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.204 129 -
Rwork0.173 2528 -
obs--94.93 %
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)
11.55310.14760.03171.36360.58360.8757-0.0277-0.05510.02730.04650.01130.01730.0028-0.01450.01630.0051-0.00020.00220.0101-0.00880.009-12.59668.2925-11.392
20.5659-0.4723-0.22951.89781.23131.4303-0.0437-0.0215-0.01050.13950.0612-0.01680.13310.0361-0.01750.01490.00070.00390.0128-0.01490.02061.3314-16.3404-24.9111
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A255 - 346
2X-RAY DIFFRACTION1A401
3X-RAY DIFFRACTION2B254 - 346
4X-RAY DIFFRACTION2B401
5X-RAY DIFFRACTION2B402

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