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- PDB-4lvt: Bcl_2-Navitoclax (ABT-263) Complex -

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Basic information

Entry
Database: PDB / ID: 4lvt
TitleBcl_2-Navitoclax (ABT-263) Complex
ComponentsApoptosis regulator Bcl-2
KeywordsAPOPTOSIS REGULATOR/INHIBITOR / 8 helices / APOPTOSIS REGULATOR-INHIBITOR complex
Function / homology
Function and homology information


negative regulation of cellular pH reduction / negative regulation of retinal cell programmed cell death / pigment granule organization / channel inhibitor activity / CD8-positive, alpha-beta T cell lineage commitment / BAD-BCL-2 complex / regulation of glycoprotein biosynthetic process / melanin metabolic process / positive regulation of skeletal muscle fiber development / positive regulation of melanocyte differentiation ...negative regulation of cellular pH reduction / negative regulation of retinal cell programmed cell death / pigment granule organization / channel inhibitor activity / CD8-positive, alpha-beta T cell lineage commitment / BAD-BCL-2 complex / regulation of glycoprotein biosynthetic process / melanin metabolic process / positive regulation of skeletal muscle fiber development / positive regulation of melanocyte differentiation / myeloid cell apoptotic process / osteoblast proliferation / cochlear nucleus development / mesenchymal cell development / retinal cell programmed cell death / positive regulation of neuron maturation / negative regulation of osteoblast proliferation / gland morphogenesis / renal system process / T cell apoptotic process / regulation of cell-matrix adhesion / stem cell development / negative regulation of calcium ion transport into cytosol / melanocyte differentiation / ear development / The NLRP1 inflammasome / dendritic cell apoptotic process / lymphoid progenitor cell differentiation / negative regulation of myeloid cell apoptotic process / negative regulation of epithelial cell apoptotic process / regulation of nitrogen utilization / BH3-only proteins associate with and inactivate anti-apoptotic BCL-2 members / B cell apoptotic process / glomerulus development / negative regulation of T cell apoptotic process / negative regulation of dendritic cell apoptotic process / oocyte development / neuron maturation / positive regulation of multicellular organism growth / metanephros development / regulation of viral genome replication / focal adhesion assembly / negative regulation of motor neuron apoptotic process / endoplasmic reticulum calcium ion homeostasis / negative regulation of ossification / negative regulation of B cell apoptotic process / response to iron ion / response to UV-B / negative regulation of mitochondrial depolarization / regulation of mitochondrial membrane permeability / calcium ion transport into cytosol / channel activity / motor neuron apoptotic process / axon regeneration / epithelial cell apoptotic process / smooth muscle cell migration / intrinsic apoptotic signaling pathway in response to oxidative stress / organ growth / NFE2L2 regulating tumorigenic genes / digestive tract morphogenesis / branching involved in ureteric bud morphogenesis / cellular response to organic substance / hair follicle morphogenesis / negative regulation of G1/S transition of mitotic cell cycle / negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / B cell lineage commitment / positive regulation of smooth muscle cell migration / B cell proliferation / pore complex / T cell homeostasis / BH3 domain binding / regulation of calcium ion transport / negative regulation of apoptotic signaling pathway / B cell homeostasis / humoral immune response / negative regulation of anoikis / extrinsic apoptotic signaling pathway via death domain receptors / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress / Estrogen-dependent nuclear events downstream of ESR-membrane signaling / Activation of BAD and translocation to mitochondria / hematopoietic stem cell differentiation / negative regulation of reactive oxygen species metabolic process / behavioral fear response / cellular response to glucose starvation / negative regulation of intrinsic apoptotic signaling pathway / skeletal muscle fiber development / positive regulation of B cell proliferation / homeostasis of number of cells within a tissue / ovarian follicle development / response to glucocorticoid / spleen development / extrinsic apoptotic signaling pathway in absence of ligand / reactive oxygen species metabolic process / ossification / axonogenesis / post-embryonic development / negative regulation of autophagy / negative regulation of cell migration / release of cytochrome c from mitochondria
Similarity search - Function
Apoptosis regulator, Bcl-2 / Apoptosis regulator, Bcl-2/ BclX / Apoptosis regulator, Bcl-2, BH4 motif, conserved site / Apoptosis regulator, Bcl-2 family BH4 motif signature. / Apoptosis regulator, Bcl-2 protein, BH4 / Bcl-2 homology region 4 / Apoptosis regulator, Bcl-2 family BH4 motif profile. / BH4 Bcl-2 homology region 4 / Apoptosis regulator, Bcl-2, BH3 motif, conserved site / Apoptosis regulator, Bcl-2 family BH3 motif signature. ...Apoptosis regulator, Bcl-2 / Apoptosis regulator, Bcl-2/ BclX / Apoptosis regulator, Bcl-2, BH4 motif, conserved site / Apoptosis regulator, Bcl-2 family BH4 motif signature. / Apoptosis regulator, Bcl-2 protein, BH4 / Bcl-2 homology region 4 / Apoptosis regulator, Bcl-2 family BH4 motif profile. / BH4 Bcl-2 homology region 4 / Apoptosis regulator, Bcl-2, BH3 motif, conserved site / Apoptosis regulator, Bcl-2 family BH3 motif signature. / Apoptosis regulator, Bcl-2, BH1 motif, conserved site / Apoptosis regulator, Bcl-2 family BH1 motif signature. / Apoptosis regulator, Bcl-2, BH2 motif, conserved site / Apoptosis regulator, Bcl-2 family BH2 motif signature. / BCL (B-Cell lymphoma); contains BH1, BH2 regions / Bcl-2 family / Bcl-2, Bcl-2 homology region 1-3 / Bcl2-like / Apoptosis regulator proteins, Bcl-2 family / BCL2-like apoptosis inhibitors family profile. / Bcl-2-like superfamily
Similarity search - Domain/homology
Chem-1XJ / Apoptosis regulator Bcl-2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsPark, C.H.
CitationJournal: NAT.MED. (N.Y.) / Year: 2013
Title: ABT-199, a potent and selective BCL-2 inhibitor, achieves antitumor activity while sparing platelets.
Authors: Souers, A.J. / Leverson, J.D. / Boghaert, E.R. / Ackler, S.L. / Catron, N.D. / Chen, J. / Dayton, B.D. / Ding, H. / Enschede, S.H. / Fairbrother, W.J. / Huang, D.C. / Hymowitz, S.G. / Jin, S. ...Authors: Souers, A.J. / Leverson, J.D. / Boghaert, E.R. / Ackler, S.L. / Catron, N.D. / Chen, J. / Dayton, B.D. / Ding, H. / Enschede, S.H. / Fairbrother, W.J. / Huang, D.C. / Hymowitz, S.G. / Jin, S. / Khaw, S.L. / Kovar, P.J. / Lam, L.T. / Lee, J. / Maecker, H.L. / Marsh, K.C. / Mason, K.D. / Mitten, M.J. / Nimmer, P.M. / Oleksijew, A. / Park, C.H. / Park, C.M. / Phillips, D.C. / Roberts, A.W. / Sampath, D. / Seymour, J.F. / Smith, M.L. / Sullivan, G.M. / Tahir, S.K. / Tse, C. / Wendt, M.D. / Xiao, Y. / Xue, J.C. / Zhang, H. / Humerickhouse, R.A. / Rosenberg, S.H. / Elmore, S.W.
History
DepositionJul 26, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 14, 2013Provider: repository / Type: Initial release
Revision 1.1Aug 2, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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 / _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: Apoptosis regulator Bcl-2
B: Apoptosis regulator Bcl-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,7164
Polymers38,7672
Non-polymers1,9492
Water3,153175
1
A: Apoptosis regulator Bcl-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,3582
Polymers19,3841
Non-polymers9751
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Apoptosis regulator Bcl-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,3582
Polymers19,3841
Non-polymers9751
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)34.770, 68.080, 65.470
Angle α, β, γ (deg.)90.00, 95.96, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Apoptosis regulator Bcl-2


Mass: 19383.594 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 1-34, 92-207 / Mutation: A2P
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BCL2 / Production host: Escherichia coli (E. coli) / References: UniProt: P10415
#2: Chemical ChemComp-1XJ / 4-(4-{[2-(4-chlorophenyl)-5,5-dimethylcyclohex-1-en-1-yl]methyl}piperazin-1-yl)-N-[(4-{[(2R)-4-(morpholin-4-yl)-1-(phenylsulfanyl)butan-2-yl]amino}-3-[(trifluoromethyl)sulfonyl]phenyl)sulfonyl]benzamide / Navitoclax


Mass: 974.613 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C47H55ClF3N5O6S3 / Comment: anticancer, inhibitor*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 175 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 1.99 Å3/Da / Density % sol: 38.13 %
Crystal growTemperature: 296 K / Method: vapor diffusion / pH: 4.2
Details: 0.5 M (NH4)2SO4, 0.1 M Na Acetate, 0.2 M NaCl, pH 4.2, VAPOR DIFFUSION, temperature 296K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-BM / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Dec 4, 2008
RadiationMonochromator: mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.05→65.12 Å / Num. all: 19201 / Num. obs: 19115 / % possible obs: 99.55 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 23.066 Å2
Reflection shellResolution: 2.05→2.17 Å / Num. unique all: 3019 / % possible all: 99.55

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
AMoREphasing
BUSTER-TNT2.5.1refinement
DENZOdata reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.05→28.92 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2219 984 5.15 %RANDOM
Rwork0.1691 ---
obs0.1716 19115 99.55 %-
all-19201 --
Displacement parametersBiso mean: 27.56 Å2
Baniso -1Baniso -2Baniso -3
1--9.80522421 Å20 Å21.95545557 Å2
2--5.96173348 Å20 Å2
3---3.84349073 Å2
Refinement stepCycle: LAST / Resolution: 2.05→28.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2324 0 130 175 2629
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONo_bond_d0.008
X-RAY DIFFRACTIONo_angle_deg0.99
X-RAY DIFFRACTIONo_dihedral_angle_d18.25
X-RAY DIFFRACTIONo_improper_angle_d
LS refinement shellResolution: 2.05→2.17 Å / Total num. of bins used: 9
RfactorNum. reflection% reflection
Rfree0.2309 155 5.13 %
Rwork0.1733 2864 -
all0.1761 3019 -
obs--99.55 %

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