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- PDB-7jgv: CRYSTAL STRUCTURE OF BCL-XL IN COMPLEX WITH COMPOUND 1620116, CRY... -

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Basic information

Entry
Database: PDB / ID: 7jgv
TitleCRYSTAL STRUCTURE OF BCL-XL IN COMPLEX WITH COMPOUND 1620116, CRYSTAL FORM 2
ComponentsBcl-2-like protein 1
KeywordsAPOPTOSIS / POPTOSIS / ALTERNATIVE SPLICING / MEMBRANE / MITOCHONDRION
Function / homology
Function and homology information


apoptotic process in bone marrow cell / The NLRP1 inflammasome / dendritic cell apoptotic process / SARS-CoV-1-mediated effects on programmed cell death / dendritic cell proliferation / positive regulation of mononuclear cell proliferation / BH3-only proteins associate with and inactivate anti-apoptotic BCL-2 members / negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage / negative regulation of dendritic cell apoptotic process / negative regulation of execution phase of apoptosis ...apoptotic process in bone marrow cell / The NLRP1 inflammasome / dendritic cell apoptotic process / SARS-CoV-1-mediated effects on programmed cell death / dendritic cell proliferation / positive regulation of mononuclear cell proliferation / BH3-only proteins associate with and inactivate anti-apoptotic BCL-2 members / negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage / negative regulation of dendritic cell apoptotic process / negative regulation of execution phase of apoptosis / negative regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway / fertilization / regulation of growth / regulation of mitochondrial membrane permeability / Bcl-2 family protein complex / BH domain binding / NFE2L2 regulating tumorigenic genes / response to cycloheximide / cellular response to alkaloid / STAT5 activation downstream of FLT3 ITD mutants / hepatocyte apoptotic process / negative regulation of release of cytochrome c from mitochondria / negative regulation of reproductive process / negative regulation of developmental process / BH3 domain binding / germ cell development / apoptotic mitochondrial changes / negative regulation of anoikis / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / ectopic germ cell programmed cell death / negative regulation of protein localization to plasma membrane / negative regulation of intrinsic apoptotic signaling pathway / negative regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / negative regulation of extrinsic apoptotic signaling pathway via death domain receptors / ovarian follicle development / extrinsic apoptotic signaling pathway in absence of ligand / negative regulation of autophagy / release of cytochrome c from mitochondria / regulation of cytokinesis / epithelial cell proliferation / response to cytokine / regulation of mitochondrial membrane potential / cellular response to amino acid stimulus / cellular response to gamma radiation / synaptic vesicle membrane / endocytosis / RAS processing / male gonad development / intrinsic apoptotic signaling pathway in response to DNA damage / spermatogenesis / nuclear membrane / Interleukin-4 and Interleukin-13 signaling / defense response to virus / neuron apoptotic process / in utero embryonic development / negative regulation of neuron apoptotic process / mitochondrial outer membrane / mitochondrial inner membrane / mitochondrial matrix / centrosome / negative regulation of apoptotic process / protein kinase binding / endoplasmic reticulum / mitochondrion / identical protein binding / cytosol / cytoplasm
Similarity search - Function
Apoptosis regulator, Bcl-X / 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-X / 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-2 family / BCL (B-Cell lymphoma); contains BH1, BH2 regions / Bcl2-like / Bcl-2, Bcl-2 homology region 1-3 / Apoptosis regulator proteins, Bcl-2 family / BCL2-like apoptosis inhibitors family profile. / Bcl-2-like superfamily
Similarity search - Domain/homology
Chem-V9S / Bcl-2-like protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.05 Å
AuthorsLee, M. / Fairlie, W.D. / Smith, B.J. / Lee, E.F.
Funding support Australia, 3items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia)Development Grant 1135421 Australia
National Health and Medical Research Council (NHMRC, Australia)Project Grant 1143974 Australia
National Health and Medical Research Council (NHMRC, Australia)Project Grant 1002227 Australia
CitationJournal: Acs Infect Dis. / Year: 2021
Title: Optimization of Benzothiazole and Thiazole Hydrazones as Inhibitors of Schistosome BCL-2.
Authors: Nguyen, W. / Lee, E.F. / Evangelista, M. / Lee, M. / Harris, T.J. / Colman, P.M. / Smith, N.A. / Williams, L.B. / Jarman, K.E. / Lowes, K.N. / Haeberli, C. / Keiser, J. / Smith, B.J. / ...Authors: Nguyen, W. / Lee, E.F. / Evangelista, M. / Lee, M. / Harris, T.J. / Colman, P.M. / Smith, N.A. / Williams, L.B. / Jarman, K.E. / Lowes, K.N. / Haeberli, C. / Keiser, J. / Smith, B.J. / Fairlie, W.D. / Sleebs, B.E.
History
DepositionJul 19, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 24, 2021Provider: repository / Type: Initial release
Revision 1.1May 26, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Bcl-2-like protein 1
B: Bcl-2-like protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,0714
Polymers35,8362
Non-polymers1,2352
Water2,882160
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4320 Å2
ΔGint-34 kcal/mol
Surface area13850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.324, 56.256, 117.756
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Bcl-2-like protein 1 / Bcl2-L-1 / Apoptosis regulator Bcl-X


Mass: 17917.959 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BCL2L1, BCL2L, BCLX / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q07817
#2: Chemical ChemComp-V9S / 6-[(8E)-8-{2-[4-(benzylcarbamoyl)-1,3-thiazol-2-yl]hydrazinylidene}-5,6,7,8-tetrahydronaphthalen-2-yl]-3-(2-phenylethoxy)pyridine-2-carboxylic acid


Mass: 617.717 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C35H31N5O4S / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 160 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 1.86 Å3/Da / Density % sol: 34 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1 M sodium acetate (pH 5.0) 10% PEG MME 2000 10% ethanol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 23, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.05→38.18 Å / Num. obs: 17473 / % possible obs: 99.7 % / Redundancy: 6 % / CC1/2: 0.995 / Net I/σ(I): 14.4
Reflection shellResolution: 2.05→2.11 Å / Num. unique obs: 1343 / CC1/2: 0.888

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
REFMAC5.8.0258refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3INQ

3inq


Resolution: 2.05→38.18 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.924 / SU B: 5.492 / SU ML: 0.145 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.252 / ESU R Free: 0.202 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2459 891 5.2 %RANDOM
Rwork0.1892 ---
obs0.1921 16407 98.85 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 75.92 Å2 / Biso mean: 28.305 Å2 / Biso min: 17.17 Å2
Baniso -1Baniso -2Baniso -3
1-1.17 Å20 Å20 Å2
2---1.19 Å20 Å2
3---0.02 Å2
Refinement stepCycle: final / Resolution: 2.05→38.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2259 0 90 160 2509
Biso mean--24.72 36.88 -
Num. residues----281
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0132443
X-RAY DIFFRACTIONr_bond_other_d0.0010.0182121
X-RAY DIFFRACTIONr_angle_refined_deg1.3581.6813319
X-RAY DIFFRACTIONr_angle_other_deg1.3341.6084897
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4525289
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.21222.754138
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.88215378
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.891514
X-RAY DIFFRACTIONr_chiral_restr0.0680.2284
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022788
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02592
LS refinement shellResolution: 2.05→2.103 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.368 64 -
Rwork0.37 1209 -
all-1273 -
obs--99.61 %

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