BMRB

Biological Magnetic Resonance Data Bank


A Repository for Data from NMR Spectroscopy on Proteins, Peptides, Nucleic Acids, and other Biomolecules
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BMRB Entry 18629

Title: Solution structure of H-RasT35S mutant protein in complex with Kobe2601   PubMed: 23630290

Deposition date: 2012-08-01 Original release date: 2013-05-20

Authors: Araki, Mitsugu; Tamura, Atsuo

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).

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:   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: MTEYKLVVVGAGGVGKSALT IQLIQNHFVDEYDPSIEDSY RKQVVIDGETCLLDILDTAG QEEYSAMRDQYMRTGEGFLC VFAINNTKSFEDIHQYREQI KRVKDSDDVPMVLVGNKCDL AARTVESRQAQDLARSYGIP YIETSAKTRQGVEDAFYTLV REIRQH

Data sets:
Data typeCount
13C chemical shifts77
1H chemical shifts238

Additional metadata:

  • Assembly
  • Samples and Experiments
  • Software
  • Spectrometers
  • Hide all

Assembly:

Entity Assembly IDEntity NameEntity ID
1H-RasT35S mutant protein1
2PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER3
3MAGNESIUM ION4
4KOB2
5water, 15
6water, 25
7water, 35

Entities:

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

1   METTHRGLUTYRLYSLEUVALVALVALGLY
2   ALAGLYGLYVALGLYLYSSERALALEUTHR
3   ILEGLNLEUILEGLNASNHISPHEVALASP
4   GLUTYRASPPROSERILEGLUASPSERTYR
5   ARGLYSGLNVALVALILEASPGLYGLUTHR
6   CYSLEULEUASPILELEUASPTHRALAGLY
7   GLNGLUGLUTYRSERALAMETARGASPGLN
8   TYRMETARGTHRGLYGLUGLYPHELEUCYS
9   VALPHEALAILEASNASNTHRLYSSERPHE
10   GLUASPILEHISGLNTYRARGGLUGLNILE
11   LYSARGVALLYSASPSERASPASPVALPRO
12   METVALLEUVALGLYASNLYSCYSASPLEU
13   ALAALAARGTHRVALGLUSERARGGLNALA
14   GLNASPLEUALAARGSERTYRGLYILEPRO
15   TYRILEGLUTHRSERALALYSTHRARGGLN
16   GLYVALGLUASPALAPHETYRTHRLEUVAL
17   ARGGLUILEARGGLNHIS

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:

NameSampleSample stateSample conditions
2D 1H-13C HSQCsample_1isotropicsample_conditions_1
3D 1H-13C NOESYsample_1isotropicsample_conditions_1
2D 1H-1H NOESYsample_2isotropicsample_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