BMRB Entry 30048

Name: Solution structure of Ras Binding Domain (RBD) of B-Raf complexed with Rigosertib (Complex I)
Published: 2016-06-20

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PDB ID: 5j18
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full, LACS
BMRB Entry DOI: doi:10.13018/BMR30048
MolProbity Validation Chart

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Nicholas Rego and David Koes
3Dmol.js: molecular visualization with WebGL
Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

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Title: Solution structure of Ras Binding Domain (RBD) of B-Raf complexed with Rigosertib (Complex I) PubMed: 27104980

Deposition date: 2016-03-29 Original release date: 2016-06-20

Authors: Dutta, K.; Vasquez-Del Carpio, R.; Aggarwal, A.; Reddy, E.

Citation: Athuluri-Divakar, S.; Vasquez-Del Carpio, R.; Dutta, K.; Baker, S.; Cosenza, S.; Basu, I.; Gupta, Y.; Reddy, M.; Ueno, L.; Hart, J.; Vogt, P.; Mulholland, D.; Guha, C.; Aggarwal, A.; Reddy, E.. "A Small Molecule RAS-Mimetic Disrupts RAS Association with Effector Proteins to Block Signaling" Cell 165, 643-655 (2016).

Assembly members:
entity_1, polymer, 92 residues, 10311.078 Da.
entity_6FS, non-polymer, 451.490 Da.

Natural source: Common Name: Human Taxonomy ID: 9606 Superkingdom: Eukaryota Kingdom: Metazoa Genus/species: Homo sapiens

Experimental source: Production method: recombinant technology Host organism: Escherichia coli

Entity Sequences (FASTA):
entity_1: GSLEVLFQGPSPQKPIVRVF LPNKQRTVVPARCGVTVRDS LKKALMMRGLIPECCAVYRI QDGEKKPIGWDTDISWLTGE ELHVEVLENVPL

Data sets:

assigned_chemical_shifts
- assigned_chemical_shifts_1

Data type	Count
13C chemical shifts	378
15N chemical shifts	76
1H chemical shifts	603

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	entity_1	1
2	entity_2	2

Entities:

Entity 1, entity_1 92 residues - 10311.078 Da.

1

GLY

SER

LEU

GLU

VAL

LEU

PHE

GLN

GLY

PRO

2

SER

PRO

GLN

LYS

PRO

ILE

VAL

ARG

VAL

PHE

3

LEU

PRO

ASN

LYS

GLN

ARG

THR

VAL

PRO

4

ALA

ARG

CYS

GLY

VAL

THR

VAL

ARG

ASP

SER

5

LEU

LYS

ALA

LEU

MET

ARG

GLY

LEU

6

ILE

PRO

GLU

CYS

ALA

VAL

TYR

ARG

ILE

7

GLN

ASP

GLY

GLU

LYS

PRO

ILE

GLY

TRP

8

ASP

THR

ASP

ILE

SER

TRP

LEU

THR

GLY

GLU

9

GLU

LEU

HIS

VAL

GLU

VAL

LEU

GLU

ASN

VAL

10

PRO

LEU

Entity 2, entity_2 - C21 H25 N O8 S - 451.490 Da.

1

6FS

Samples:

sample_1: B-RAF-RBD:Rigosertib Complex I, [U-99% 13C; U-99% 15N], 200 uM; 6FS ligand, [U-99% 13C; U-99% 15N], 200 uM; NaCl 200 mM

sample_conditions_1: ionic strength: 200 mM; pH: 7.4; pressure: 1 atm; temperature: 298 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-15N HSQC	sample_1	isotropic	sample_conditions_1
2D 1H-13C HSQC	sample_1	isotropic	sample_conditions_1
3D 1H-15N NOESY	sample_1	isotropic	sample_conditions_1
3D 1H-13C NOESY aliphatic	sample_1	isotropic	sample_conditions_1
3D 1H-13C NOESY aromatic	sample_1	isotropic	sample_conditions_1

Software:

ARIA, Linge, O'Donoghue and Nilges - refinement, structure calculation

NMRView, Johnson, One Moon Scientific - chemical shift assignment, peak picking

NMR spectrometers:

Bruker Avance 800 MHz
Bruker Avance 900 MHz

Download simulated HSQC data in one of the following formats:
CSV: Backbone or all simulated shifts
SPARKY: Backbone or all simulated shifts