[English] 日本語
Yorodumi- PDB-8av9: INDUCED MYELOID LEUKEMIA CELL DIFFERENTIATION PROTEIN FABCOMPLEX ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8av9 | ||||||
---|---|---|---|---|---|---|---|
Title | INDUCED MYELOID LEUKEMIA CELL DIFFERENTIATION PROTEIN FABCOMPLEX IN COMPLEX WITH COMPOUND 1 | ||||||
Components |
| ||||||
Keywords | APOPTOSIS / MCL1 / FAB / MACROCYCLE / MCL1-FAB_55_C6HIS / IMMUNE SYSTEM | ||||||
Function / homology | Function and homology information positive regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway / cell fate determination / cellular homeostasis / Bcl-2 family protein complex / mitochondrial fusion / BH domain binding / BH3 domain binding / protein transmembrane transporter activity / negative regulation of anoikis / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand ...positive regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway / cell fate determination / cellular homeostasis / Bcl-2 family protein complex / mitochondrial fusion / BH domain binding / BH3 domain binding / protein transmembrane transporter activity / negative regulation of anoikis / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / extrinsic apoptotic signaling pathway in absence of ligand / negative regulation of autophagy / release of cytochrome c from mitochondria / response to cytokine / channel activity / intrinsic apoptotic signaling pathway in response to DNA damage / Signaling by ALK fusions and activated point mutants / Interleukin-4 and Interleukin-13 signaling / regulation of apoptotic process / mitochondrial outer membrane / positive regulation of apoptotic process / protein heterodimerization activity / DNA damage response / negative regulation of apoptotic process / mitochondrion / nucleoplasm / membrane / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.99 Å | ||||||
Authors | Hargreaves, D. | ||||||
Funding support | 1items
| ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2023 Title: Design of rigid protein-protein interaction inhibitors enables targeting of undruggable Mcl-1. Authors: Hargreaves, D. / Carbajo, R.J. / Bodnarchuk, M.S. / Embrey, K. / Rawlins, P.B. / Packer, M. / Degorce, S.L. / Hird, A.W. / Johannes, J.W. / Chiarparin, E. / Schade, M. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 8av9.cif.gz | 134.8 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb8av9.ent.gz | 101.1 KB | Display | PDB format |
PDBx/mmJSON format | 8av9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8av9_validation.pdf.gz | 803.1 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 8av9_full_validation.pdf.gz | 808 KB | Display | |
Data in XML | 8av9_validation.xml.gz | 25.2 KB | Display | |
Data in CIF | 8av9_validation.cif.gz | 37.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/av/8av9 ftp://data.pdbj.org/pub/pdb/validation_reports/av/8av9 | HTTPS FTP |
-Related structure data
Similar structure data | Similarity search - Function & homologyF&H Search |
---|
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 18227.592 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: MCL1, BCL2L3 / Production host: Komagataella pastoris (fungus) / References: UniProt: Q07820 |
---|---|
#2: Antibody | Mass: 24488.490 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Production host: Komagataella pastoris (fungus) |
#3: Antibody | Mass: 25318.660 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Production host: Komagataella pastoris (fungus) |
#4: Chemical | ChemComp-VF8 / ( |
#5: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.25 Å3/Da / Density % sol: 45.36 % |
---|---|
Crystal grow | Temperature: 310 K / Method: vapor diffusion / Details: 15% Peg2kMME, PCTP 0.1M pH 6.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.98 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 4, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 1.99→70.58 Å / Num. obs: 41926 / % possible obs: 99.7 % / Redundancy: 3.2 % / Biso Wilson estimate: 28.26 Å2 / Rmerge(I) obs: 0.079 / Net I/σ(I): 6.7 |
Reflection shell | Resolution: 1.99→2.04 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.577 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 41926 / % possible all: 99.7 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: in house Resolution: 1.99→70.58 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.915 / SU R Cruickshank DPI: 0.206 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.212 / SU Rfree Blow DPI: 0.186 / SU Rfree Cruickshank DPI: 0.185
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 102.16 Å2 / Biso mean: 36.79 Å2 / Biso min: 11.48 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.3 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.99→70.58 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.99→2 Å / Rfactor Rfree error: 0 / Total num. of bins used: 51
|