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- PDB-5ct7: BRAF in Complex with RAF265 -

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Basic information

Entry
Database: PDB / ID: 5ct7
TitleBRAF in Complex with RAF265
ComponentsSerine/threonine-protein kinase B-raf
KeywordsTRANSFERASE / kinase
Function / homology
Function and homology information


CD4-positive, alpha-beta T cell differentiation / positive regulation of axon regeneration / CD4-positive or CD8-positive, alpha-beta T cell lineage commitment / negative regulation of synaptic vesicle exocytosis / Signalling to p38 via RIT and RIN / head morphogenesis / ARMS-mediated activation / endothelial cell apoptotic process / myeloid progenitor cell differentiation / SHOC2 M1731 mutant abolishes MRAS complex function ...CD4-positive, alpha-beta T cell differentiation / positive regulation of axon regeneration / CD4-positive or CD8-positive, alpha-beta T cell lineage commitment / negative regulation of synaptic vesicle exocytosis / Signalling to p38 via RIT and RIN / head morphogenesis / ARMS-mediated activation / endothelial cell apoptotic process / myeloid progenitor cell differentiation / SHOC2 M1731 mutant abolishes MRAS complex function / Gain-of-function MRAS complexes activate RAF signaling / positive regulation of D-glucose transmembrane transport / negative regulation of fibroblast migration / establishment of protein localization to membrane / positive regulation of axonogenesis / regulation of T cell differentiation / Negative feedback regulation of MAPK pathway / Frs2-mediated activation / stress fiber assembly / face development / MAP kinase kinase activity / thyroid gland development / synaptic vesicle exocytosis / somatic stem cell population maintenance / positive regulation of peptidyl-serine phosphorylation / MAP kinase kinase kinase activity / negative regulation of endothelial cell apoptotic process / postsynaptic modulation of chemical synaptic transmission / positive regulation of stress fiber assembly / ERK1 and ERK2 cascade / positive regulation of substrate adhesion-dependent cell spreading / substrate adhesion-dependent cell spreading / cellular response to calcium ion / thymus development / animal organ morphogenesis / Spry regulation of FGF signaling / RAF activation / Signaling by high-kinase activity BRAF mutants / MAP2K and MAPK activation / visual learning / Negative regulation of MAPK pathway / centriolar satellite / cellular response to xenobiotic stimulus / epidermal growth factor receptor signaling pathway / long-term synaptic potentiation / Signaling by RAF1 mutants / Signaling by moderate kinase activity BRAF mutants / Paradoxical activation of RAF signaling by kinase inactive BRAF / Signaling downstream of RAS mutants / Signaling by BRAF and RAF1 fusions / T cell differentiation in thymus / presynapse / T cell receptor signaling pathway / MAPK cascade / regulation of cell population proliferation / cell body / scaffold protein binding / negative regulation of neuron apoptotic process / neuron projection / positive regulation of ERK1 and ERK2 cascade / protein phosphorylation / non-specific serine/threonine protein kinase / protein kinase activity / postsynapse / cilium / ciliary basal body / protein serine kinase activity / intracellular membrane-bounded organelle / protein serine/threonine kinase activity / calcium ion binding / positive regulation of gene expression / negative regulation of apoptotic process / glutamatergic synapse / mitochondrion / zinc ion binding / ATP binding / identical protein binding / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Raf-like Ras-binding domain / Raf-like Ras-binding / Ras-binding domain (RBD) profile. / Raf-like Ras-binding domain / Diacylglycerol/phorbol-ester binding / : / Phorbol esters/diacylglycerol binding domain (C1 domain) / Zinc finger phorbol-ester/DAG-type signature. / Zinc finger phorbol-ester/DAG-type profile. / Protein kinase C conserved region 1 (C1) domains (Cysteine-rich domains) ...Raf-like Ras-binding domain / Raf-like Ras-binding / Ras-binding domain (RBD) profile. / Raf-like Ras-binding domain / Diacylglycerol/phorbol-ester binding / : / Phorbol esters/diacylglycerol binding domain (C1 domain) / Zinc finger phorbol-ester/DAG-type signature. / Zinc finger phorbol-ester/DAG-type profile. / Protein kinase C conserved region 1 (C1) domains (Cysteine-rich domains) / Protein kinase C-like, phorbol ester/diacylglycerol-binding domain / C1-like domain superfamily / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein tyrosine and serine/threonine kinase / Ubiquitin-like domain superfamily / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-55J / Serine/threonine-protein kinase B-raf
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.17 Å
AuthorsAppleton, B.A.
CitationJournal: Acs Med.Chem.Lett. / Year: 2015
Title: Discovery of RAF265: A Potent mut-B-RAF Inhibitor for the Treatment of Metastatic Melanoma.
Authors: Williams, T.E. / Subramanian, S. / Verhagen, J. / McBride, C.M. / Costales, A. / Sung, L. / Antonios-McCrea, W. / McKenna, M. / Louie, A.K. / Ramurthy, S. / Levine, B. / Shafer, C.M. / ...Authors: Williams, T.E. / Subramanian, S. / Verhagen, J. / McBride, C.M. / Costales, A. / Sung, L. / Antonios-McCrea, W. / McKenna, M. / Louie, A.K. / Ramurthy, S. / Levine, B. / Shafer, C.M. / Machajewski, T. / Renhowe, P.A. / Appleton, B.A. / Amiri, P. / Chou, J. / Stuart, D. / Aardalen, K. / Poon, D.
History
DepositionJul 23, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 9, 2015Provider: repository / Type: Initial release
Revision 1.1Oct 7, 2015Group: Database references
Revision 1.2Mar 6, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Serine/threonine-protein kinase B-raf
B: Serine/threonine-protein kinase B-raf
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,8654
Polymers63,8282
Non-polymers1,0372
Water00
1
A: Serine/threonine-protein kinase B-raf
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,4322
Polymers31,9141
Non-polymers5181
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Serine/threonine-protein kinase B-raf
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,4322
Polymers31,9141
Non-polymers5181
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)109.380, 109.380, 158.130
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Serine/threonine-protein kinase B-raf / Proto-oncogene B-Raf / p94 / v-Raf murine sarcoma viral oncogene homolog B1


Mass: 31913.881 Da / Num. of mol.: 2 / Fragment: kinase domain (UNP residues 445-723)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BRAF, BRAF1, RAFB1 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: P15056, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-55J / 1-methyl-5-({2-[5-(trifluoromethyl)-1H-imidazol-2-yl]pyridin-4-yl}oxy)-N-[4-(trifluoromethyl)phenyl]-1H-benzimidazol-2-amine


Mass: 518.414 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C24H16F6N6O

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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: 3.71 Å3/Da / Density % sol: 66.8 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.4 / Details: 12% PEG8000, 0.1 M NaCl, and 0.1 M Tris pH 8.4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 9, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.17→48.91 Å / Num. all: 118477 / Num. obs: 16841 / % possible obs: 99.9 % / Redundancy: 7 % / Rmerge(I) obs: 0.118 / Net I/σ(I): 17
Reflection shellResolution: 3.17→3.29 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.72 / Mean I/σ(I) obs: 2.8 / % possible all: 99.9

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Processing

Software
NameVersionClassification
BUSTER2.11.4refinement
PDB_EXTRACT3.15data extraction
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.17→48.91 Å / Cor.coef. Fo:Fc: 0.9302 / Cor.coef. Fo:Fc free: 0.8963 / SU R Cruickshank DPI: 1.679 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 2.07 / SU Rfree Blow DPI: 0.335 / SU Rfree Cruickshank DPI: 0.339
RfactorNum. reflection% reflectionSelection details
Rfree0.2173 868 5.16 %RANDOM
Rwork0.1811 ---
obs0.1829 16811 99.43 %-
Displacement parametersBiso max: 159.83 Å2 / Biso mean: 73.59 Å2 / Biso min: 37.25 Å2
Baniso -1Baniso -2Baniso -3
1-5.3218 Å20 Å20 Å2
2--5.3218 Å20 Å2
3----10.6437 Å2
Refine analyzeLuzzati coordinate error obs: 0.577 Å
Refinement stepCycle: final / Resolution: 3.17→48.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4010 0 74 0 4084
Biso mean--60.22 --
Num. residues----511
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1444SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes90HARMONIC2
X-RAY DIFFRACTIONt_gen_planes669HARMONIC5
X-RAY DIFFRACTIONt_it4178HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion541SEMIHARMONIC5
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_contact4883SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d4178HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg5664HARMONIC21.13
X-RAY DIFFRACTIONt_omega_torsion2.86
X-RAY DIFFRACTIONt_other_torsion20.07
LS refinement shellResolution: 3.17→3.39 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.2455 162 5.56 %
Rwork0.2162 2754 -
all0.218 2916 -
obs--99.43 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.9335-0.97062.24811.9503-0.57222.36550.1278-0.2595-0.31660.15040.0970.25420.0426-0.0908-0.2248-0.2-0.0002-0.0085-0.07280.15570.0154-15.778510.61260.7887
22.5818-1.47521.07481.7441-1.39751.96170.0289-0.1829-0.1953-0.05760.13370.1488-0.1232-0.0796-0.1625-0.20480.00610.0066-0.03550.10650.0227-39.709330.0595-14.3894
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A449 - 721
2X-RAY DIFFRACTION2{ B|* }B449 - 721

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