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- PDB-8x62: crystal structure of human Mcl-1 kinase domain in complex with RM1 -

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Basic information

Entry
Database: PDB / ID: 8x62
Titlecrystal structure of human Mcl-1 kinase domain in complex with RM1
ComponentsInduced myeloid leukemia cell differentiation protein Mcl-1
KeywordsTRANSFERASE / INHIBITOR / TEANSFERASE
Function / homology
Function and homology information


positive regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway / cell fate determination / cellular homeostasis / mitochondrial fusion / Bcl-2 family protein complex / BH3 domain binding / negative regulation of anoikis / protein transmembrane transporter activity / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / extrinsic apoptotic signaling pathway in absence of ligand ...positive regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway / cell fate determination / cellular homeostasis / mitochondrial fusion / Bcl-2 family protein complex / BH3 domain binding / negative regulation of anoikis / protein transmembrane transporter activity / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / extrinsic apoptotic signaling pathway in absence of ligand / response to cytokine / negative regulation of autophagy / release of cytochrome c from mitochondria / intrinsic apoptotic signaling pathway in response to DNA damage / Signaling by ALK fusions and activated point mutants / positive regulation of neuron apoptotic process / channel activity / 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 / nucleus / membrane / cytosol / cytoplasm
Similarity search - Function
Apoptosis regulator, Mcl-1 / 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 ...Apoptosis regulator, Mcl-1 / 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
: / Induced myeloid leukemia cell differentiation protein Mcl-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.80339461801 Å
AuthorsZhang, Z.M. / Wang, L.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: crystal structure of human Mcl-1 kinase domain in complex with RM1
Authors: Zhang, Z.M. / Wang, L.
History
DepositionNov 20, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 21, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Induced myeloid leukemia cell differentiation protein Mcl-1
B: Induced myeloid leukemia cell differentiation protein Mcl-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,1353
Polymers34,5592
Non-polymers5761
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)52.761, 56.011, 66.097
Angle α, β, γ (deg.)90.0, 112.771, 90.0
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein Induced myeloid leukemia cell differentiation protein Mcl-1


Mass: 17279.730 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MCL1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q07820
#2: Chemical ChemComp-YO0 / 1-[7-[1,5-dimethyl-3-(phenoxymethyl)pyrazol-4-yl]-3-(3-naphthalen-1-yloxypropyl)-1~{H}-indol-2-yl]-2,2-bis(oxidanyl)ethanone


Mass: 575.654 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C35H33N3O5 / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationN
Nonpolymer detailsTwo hydroxyl groups of YO0 could lose one water and transfer to glyoxal group which will react with ...Two hydroxyl groups of YO0 could lose one water and transfer to glyoxal group which will react with two amino groups of Arg263 and lose one water again.

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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: 2.61 Å3/Da / Density % sol: 52.93 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 0.1M Sodium citrate tribasic dihydrate (pH 5.5-6.5), 18% (v/v) 2-propanol and 13~20% (w/v) PEG 4000.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CAMD / Beamline: GCPCC / Wavelength: 0.987 Å
DetectorType: DECTRIS PILATUS 300K / Detector: PIXEL / Date: Apr 1, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 2.8→32.4 Å / Num. obs: 8826 / % possible obs: 99.6 % / Redundancy: 3.3 % / Biso Wilson estimate: 68.5208719596 Å2 / CC1/2: 0.948 / Net I/σ(I): 7.89
Reflection shellResolution: 2.8→2.9 Å / CC1/2: 0.948

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Processing

Software
NameVersionClassification
PHENIX1.9_1692+SVNrefinement
PHENIX1.9_1692+SVNrefinement
HKL-3000data reduction
HKL-3000data scaling
PHASESphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.80339461801→32.4 Å / SU ML: 0.48112058671 / Cross valid method: FREE R-VALUE / σ(F): 1.36061523847 / Phase error: 35.5689716979
RfactorNum. reflection% reflection
Rfree0.288141854856 882 9.99433427762 %
Rwork0.254963694383 7943 -
obs0.255339728218 8826 99.4366197183 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 75.7049913713 Å2
Refinement stepCycle: LAST / Resolution: 2.80339461801→32.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2207 0 41 0 2248
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.003263700448382288
X-RAY DIFFRACTIONf_angle_d0.7556276405943113
X-RAY DIFFRACTIONf_chiral_restr0.020560898052361
X-RAY DIFFRACTIONf_plane_restr0.00235195112254390
X-RAY DIFFRACTIONf_dihedral_angle_d14.9391721182779
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8034-2.97890.3994157327041420.3302179288641288X-RAY DIFFRACTION97.9452054795
2.9789-3.20870.3736789755951460.3074718872571317X-RAY DIFFRACTION99.7273346967
3.2087-3.53130.3226691370261500.2815656041881318X-RAY DIFFRACTION99.7282608696
3.5313-4.04140.297921757741500.2622820669381313X-RAY DIFFRACTION99.7273346967
4.0414-5.08860.2819758954981460.2404761650141341X-RAY DIFFRACTION99.9327956989
5.0886-32.3980.2405538182471480.2287173887591366X-RAY DIFFRACTION99.6052631579

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