BMRB Entry 18629

Name: Solution structure of H-RasT35S mutant protein in complex with Kobe2601
Published: 2013-05-20

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PDB ID: 2lwi
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR18629
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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 H-RasT35S mutant protein in complex with Kobe2601

Deposition date:

2012-08-01

Original release date:

2013-05-20

Authors:

Araki, Mitsugu; Tamura, Atsuo

Citation:

Citation: Shima, Fumi; Yoshikawa, Yoko; Ye, Min; Araki, Mitsugu; Matsumoto, Shigeyuki; Liao, Jingling; Hu, Lizhi; Sugimoto, Takeshi; Ijiri, Yuichi; Takeda, Azusa; Nishiyama, Yuko; Sato, Chie; Muraoka, Shin; Tamura, Atsuo; Osoda, Tsutomu; Tsuda, Ken-ichiro; Miyakawa, Tomoya; Fukunishi, Hiroaki; Shimada, Jiro; Kumasaka, Takashi; Yamamotog, Masaki; Kataoka, Tohru. "In silico discovery of small-molecule Ras inhibitors that display antitumor activity by blocking the Ras-effector interaction" Proc. Natl. Acad. Sci. U. S. A. 110, 8182-8187 (2013).
PubMed: 23630290

Assembly members:

Assembly members:
entity_1, polymer, 166 residues, 18861.303 Da.
2-(2,4-dinitrophenyl)-N-(4-fluorophenyl)hydrazinecarbothioamide, non-polymer, 351.313 Da.
PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER, non-polymer, 522.196 Da.
MAGNESIUM ION, non-polymer, 24.305 Da.
WATER, water, 18.015 Da.

Natural source:

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

Experimental source:

Experimental source: Production method: recombinant technology Host organism: Escherichia coli Vector: pGEX-6P-1

Entity Sequences (FASTA):

Entity Sequences (FASTA):
entity_1: MTEYKLVVVGAGGVGKSALT IQLIQNHFVDEYDPSIEDSY RKQVVIDGETCLLDILDTAG QEEYSAMRDQYMRTGEGFLC VFAINNTKSFEDIHQYREQI KRVKDSDDVPMVLVGNKCDL AARTVESRQAQDLARSYGIP YIETSAKTRQGVEDAFYTLV REIRQH

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
13C chemical shifts	77
1H chemical shifts	238

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	H-RasT35S mutant protein	1
2	PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER	3
3	MAGNESIUM ION	4
4	KOB	2
5	water, 1	5
6	water, 2	5
7	water, 3	5

Entities:

Entity 1, H-RasT35S mutant protein 166 residues - 18861.303 Da.

1

MET

THR

GLU

TYR

LYS

LEU

VAL

GLY

2

ALA

GLY

VAL

GLY

LYS

SER

ALA

LEU

THR

3

ILE

GLN

LEU

ILE

GLN

ASN

HIS

PHE

VAL

ASP

4

GLU

TYR

ASP

PRO

SER

ILE

GLU

ASP

SER

TYR

5

ARG

LYS

GLN

VAL

ILE

ASP

GLY

GLU

THR

6

CYS

LEU

ASP

ILE

LEU

ASP

THR

ALA

GLY

7

GLN

GLU

TYR

SER

ALA

MET

ARG

ASP

GLN

8

TYR

MET

ARG

THR

GLY

GLU

GLY

PHE

LEU

CYS

9

VAL

PHE

ALA

ILE

ASN

THR

LYS

SER

PHE

10

GLU

ASP

ILE

HIS

GLN

TYR

ARG

GLU

GLN

ILE

11

LYS

ARG

VAL

LYS

ASP

SER

ASP

VAL

PRO

12

MET

VAL

LEU

VAL

GLY

ASN

LYS

CYS

ASP

LEU

13

ALA

ARG

THR

VAL

GLU

SER

ARG

GLN

ALA

14

GLN

ASP

LEU

ALA

ARG

SER

TYR

GLY

ILE

PRO

15

TYR

ILE

GLU

THR

SER

ALA

LYS

THR

ARG

GLN

16

GLY

VAL

GLU

ASP

ALA

PHE

TYR

THR

LEU

VAL

17

ARG

GLU

ILE

ARG

GLN

HIS

Entity 3, PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER - C10 H17 N6 O13 P3 - 522.196 Da.

1

GNP

Entity 4, MAGNESIUM ION - Mg - 24.305 Da.

1

MG

Entity 2, KOB - C13 H10 F N5 O4 S - 351.313 Da.

1

KOB

Entity 5, water, 1 - 18.015 Da.

1

HOH

Samples:

sample_1: H-RasT35S, [U-98% 13C; U-98% 15N], 1 mM; PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER 1 mM; MAGNESIUM ION 8 mM; sodium chloride 120 mM; sodium phosphate 20 mM; KOB 3.8 mM; D2O 80%; DMSO_d6 20%

sample_2: H-RasT35S 1 mM; PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER 1 mM; MAGNESIUM ION 8 mM; sodium chloride 120 mM; sodium phosphate 20 mM; KOB 3.8 mM; D2O 80%; DMSO_d6 20%

sample_conditions_1: ionic strength: 0.22 M; pH: 6.8; pressure: 1 atm; temperature: 278 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-13C HSQC	sample_1	isotropic	sample_conditions_1
3D 1H-13C NOESY	sample_1	isotropic	sample_conditions_1
2D 1H-1H NOESY	sample_2	isotropic	sample_conditions_1

Software:

CYANA v2.1, Guntert, Mumenthaler and Wuthrich - structure solution

CNS v1.2, Brunger, Adams, Clore, Gros, Nilges and Read - refinement

NMRPipe, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - processing

SPARKY, Goddard - peak picking

NMR spectrometers:

Bruker DMX 750 MHz
Bruker Avance 600 MHz