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- PDB-5mes: MCL1 FAB COMPLEX IN COMPLEX WITH COMPOUND 29 -

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Basic information

Entry
Database: PDB / ID: 5mes
TitleMCL1 FAB COMPLEX IN COMPLEX WITH COMPOUND 29
Components
  • Heavy Chain
  • Induced myeloid leukemia cell differentiation protein Mcl-1 homolog,Induced myeloid leukemia cell differentiation protein Mcl-1
  • Light Chain
KeywordsIMMUNE SYSTEM / MCL1 / FAB / macrocycle / MCL1-FAB_55_C6HIS
Function / homology
Function and homology information


BH domain binding / positive regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway / cellular homeostasis / cell fate determination / mitochondrial fusion / channel activity / Bcl-2 family protein complex / BH3 domain binding / negative regulation of anoikis / protein transmembrane transporter activity ...BH domain binding / positive regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway / cellular homeostasis / cell fate determination / mitochondrial fusion / channel activity / 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 / negative regulation of autophagy / release of cytochrome c from mitochondria / response to cytokine / Signaling by ALK fusions and activated point mutants / intrinsic apoptotic signaling pathway in response to DNA damage / regulation of apoptotic process / Interleukin-4 and Interleukin-13 signaling / mitochondrial outer membrane / cell differentiation / protein dimerization activity / positive regulation of apoptotic process / protein heterodimerization activity / DNA damage response / protein-containing complex binding / negative regulation of apoptotic process / protein homodimerization activity / mitochondrion / nucleoplasm / membrane / nucleus / cytosol / cytoplasm
Similarity search - Function
Apoptosis regulator, Mcl-1 / Blc2-like / Apoptosis Regulator Bcl-x / 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 ...Apoptosis regulator, Mcl-1 / Blc2-like / Apoptosis Regulator Bcl-x / 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 / Immunoglobulins / Immunoglobulin-like / Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Chem-7LT / Induced myeloid leukemia cell differentiation protein Mcl-1 homolog / Induced myeloid leukemia cell differentiation protein Mcl-1
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.24 Å
AuthorsHargreaves, D.
CitationJournal: ACS Med Chem Lett / Year: 2017
Title: Structure Based Design of Non-Natural Peptidic Macrocyclic Mcl-1 Inhibitors.
Authors: Johannes, J.W. / Bates, S. / Beigie, C. / Belmonte, M.A. / Breen, J. / Cao, S. / Centrella, P.A. / Clark, M.A. / Cuozzo, J.W. / Dumelin, C.E. / Ferguson, A.D. / Habeshian, S. / Hargreaves, D. ...Authors: Johannes, J.W. / Bates, S. / Beigie, C. / Belmonte, M.A. / Breen, J. / Cao, S. / Centrella, P.A. / Clark, M.A. / Cuozzo, J.W. / Dumelin, C.E. / Ferguson, A.D. / Habeshian, S. / Hargreaves, D. / Joubran, C. / Kazmirski, S. / Keefe, A.D. / Lamb, M.L. / Lan, H. / Li, Y. / Ma, H. / Mlynarski, S. / Packer, M.J. / Rawlins, P.B. / Robbins, D.W. / Shen, H. / Sigel, E.A. / Soutter, H.H. / Su, N. / Troast, D.M. / Wang, H. / Wickson, K.F. / Wu, C. / Zhang, Y. / Zhao, Q. / Zheng, X. / Hird, A.W.
History
DepositionNov 16, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 18, 2017Provider: repository / Type: Initial release
Revision 1.1Mar 1, 2017Group: Database references
Revision 1.2Mar 8, 2017Group: Database references

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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 homolog,Induced myeloid leukemia cell differentiation protein Mcl-1
H: Heavy Chain
L: Light Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,6564
Polymers66,8743
Non-polymers7831
Water3,639202
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4940 Å2
ΔGint-26 kcal/mol
Surface area25930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)168.470, 40.330, 102.840
Angle α, β, γ (deg.)90.00, 126.11, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11L-345-

HOH

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Components

#1: Protein Induced myeloid leukemia cell differentiation protein Mcl-1 homolog,Induced myeloid leukemia cell differentiation protein Mcl-1 / Bcl-2-related protein EAT/mcl1 / Bcl-2-like protein 3 / Bcl2-L-3 / Bcl-2-related protein EAT/mcl1 / mcl1/EAT


Mass: 18227.592 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse), (gene. exp.) Homo sapiens (human)
Gene: Mcl1, MCL1, BCL2L3 / Production host: Komagataella pastoris (fungus) / References: UniProt: P97287, UniProt: Q07820
#2: Antibody Heavy Chain


Mass: 24488.490 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Komagataella pastoris (fungus)
#3: Antibody Light Chain /


Mass: 24157.469 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Komagataella pastoris (fungus)
#4: Chemical ChemComp-7LT / (5~{R},13~{S},17~{S})-5-[[4-chloranyl-3-(2-phenylethyl)phenyl]methyl]-13-[(4-chlorophenyl)methyl]-8-methyl-1,4,8,12,16-pentazatricyclo[15.8.1.0^{20,25}]hexacosa-20(25),21,23-triene-3,7,15,26-tetrone


Mass: 782.797 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C44H49Cl2N5O4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 202 / Source method: isolated from a natural source / Formula: H2O

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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: 2.1 Å3/Da / Density % sol: 41.36 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: PEG 8K 10%w/v, PEG 1500 10%w/v

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97626 Å
DetectorType: DECTRIS PILATUS3 X 1M / Detector: PIXEL / Date: Apr 15, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97626 Å / Relative weight: 1
ReflectionResolution: 2.24→81.02 Å / Num. obs: 27132 / % possible obs: 99.4 % / Redundancy: 3.3 % / Biso Wilson estimate: 49.23 Å2 / Rmerge(I) obs: 0.06 / Rpim(I) all: 0.057 / Rrim(I) all: 0.083 / Net I/σ(I): 11.7
Reflection shellResolution: 2.24→2.3 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.709 / CC1/2: 0.5

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Processing

Software
NameVersionClassification
BUSTER2.11.6refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.24→81.02 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.93 / Rfactor Rfree error: 0 / SU R Cruickshank DPI: 0.301 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.308 / SU Rfree Blow DPI: 0.213 / SU Rfree Cruickshank DPI: 0.214
RfactorNum. reflection% reflectionSelection details
Rfree0.23 1326 4.89 %RANDOM
Rwork0.18 ---
obs0.182 27131 99 %-
Displacement parametersBiso mean: 52.02 Å2
Baniso -1Baniso -2Baniso -3
1-0.4043 Å20 Å20.4612 Å2
2---0.4902 Å20 Å2
3---0.0859 Å2
Refine analyzeLuzzati coordinate error obs: 0.27 Å
Refinement stepCycle: LAST / Resolution: 2.24→81.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4404 0 55 202 4661
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.014583HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.116235HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1553SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes92HARMONIC2
X-RAY DIFFRACTIONt_gen_planes674HARMONIC5
X-RAY DIFFRACTIONt_it4583HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.21
X-RAY DIFFRACTIONt_other_torsion19.6
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion604SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact5284SEMIHARMONIC4
LS refinement shellResolution: 2.24→2.32 Å / Rfactor Rfree error: 0 / Total num. of bins used: 14
RfactorNum. reflection% reflection
Rfree0.299 131 4.68 %
Rwork0.23 2670 -
all0.234 2801 -
obs--99.07 %

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