- PDB-3qkd: Crystal structure of Bcl-xL in complex with a Quinazoline sulfona... -
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Open data
ID or keywords:
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Basic information
Entry
Database: PDB / ID: 3qkd
Title
Crystal structure of Bcl-xL in complex with a Quinazoline sulfonamide inhibitor
Components
Bcl-2-like protein 1
Keywords
APOPTOSIS/INHIBITOR / Bcl-2 family fold / APOPTOSIS-INHIBITOR complex
Function / homology
Function and homology information
apoptotic process in bone marrow cell / SARS-CoV-1-mediated effects on programmed cell death / The NLRP1 inflammasome / dendritic cell apoptotic process / 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 execution phase of apoptosis / negative regulation of dendritic cell apoptotic process ...apoptotic process in bone marrow cell / SARS-CoV-1-mediated effects on programmed cell death / The NLRP1 inflammasome / dendritic cell apoptotic process / 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 execution phase of apoptosis / negative regulation of dendritic cell apoptotic process / negative regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway / fertilization / regulation of mitochondrial membrane permeability / regulation of growth / negative regulation of protein localization to plasma membrane / Bcl-2 family protein complex / BH domain binding / NFE2L2 regulating tumorigenic genes / response to cycloheximide / STAT5 activation downstream of FLT3 ITD mutants / cellular response to alkaloid / 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 endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / negative regulation of 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 / regulation of mitochondrial membrane potential / epithelial cell proliferation / response to cytokine / cellular response to amino acid stimulus / cellular response to gamma radiation / synaptic vesicle membrane / RAS processing / endocytosis / male gonad development / intrinsic apoptotic signaling pathway in response to DNA damage / spermatogenesis / nuclear membrane / Interleukin-4 and Interleukin-13 signaling / neuron apoptotic process / defense response to virus / 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 (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
Resolution: 2.02→43.9 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.934 / SU B: 3.875 / SU ML: 0.107 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.153 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.23093
1450
5.2 %
RANDOM
Rwork
0.19184
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-
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all
0.19384
27379
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obs
0.19384
26408
96.45 %
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Solvent computation
Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parameters
Biso mean: 28.758 Å2
Baniso -1
Baniso -2
Baniso -3
1-
-0.59 Å2
0 Å2
0 Å2
2-
-
1.68 Å2
0 Å2
3-
-
-
-1.09 Å2
Refinement step
Cycle: LAST / Resolution: 2.02→43.9 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
2293
0
123
210
2626
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.01
0.021
2523
X-RAY DIFFRACTION
r_angle_refined_deg
1.152
1.973
3425
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
5
5
288
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
34.532
23.759
133
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
15.603
15
387
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
16.838
15
18
X-RAY DIFFRACTION
r_chiral_restr
0.077
0.2
343
X-RAY DIFFRACTION
r_gen_planes_refined
0.004
0.02
1970
X-RAY DIFFRACTION
r_nbd_refined
0.186
0.2
1193
X-RAY DIFFRACTION
r_nbtor_refined
0.308
0.2
1730
X-RAY DIFFRACTION
r_xyhbond_nbd_refined
0.167
0.2
185
X-RAY DIFFRACTION
r_symmetry_vdw_refined
0.168
0.2
39
X-RAY DIFFRACTION
r_symmetry_hbond_refined
0.142
0.2
24
X-RAY DIFFRACTION
r_mcbond_it
0.62
1.5
1453
X-RAY DIFFRACTION
r_mcangle_it
1.078
2
2253
X-RAY DIFFRACTION
r_scbond_it
1.461
3
1328
X-RAY DIFFRACTION
r_scangle_it
2.391
4.5
1168
LS refinement shell
Resolution: 2.02→2.072 Å / Total num. of bins used: 20
Rfactor
Num. reflection
% reflection
Rfree
0.279
103
-
Rwork
0.273
1746
-
obs
-
-
87.51 %
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