BMRB Entry 18629
Click here to enlarge.
PDB ID:
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR18629
MolProbity Validation Chart
NMR-STAR file interactive viewer.
NMR-STAR v3 text file.
NMR-STAR v2.1 text file (deprecated)
XML gzip file.
RDF gzip file.
All files associated with the entry
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
- assigned_chemical_shifts
| Data type | Count |
| 13C chemical shifts | 77 |
| 1H chemical shifts | 238 |
Additional metadata:
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 | VAL | VAL | GLY | ||||
| 2 | ALA | GLY | 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 | VAL | ILE | ASP | GLY | GLU | THR | ||||
| 6 | CYS | LEU | LEU | ASP | ILE | LEU | ASP | THR | ALA | GLY | ||||
| 7 | GLN | GLU | 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 | ASN | THR | LYS | SER | PHE | ||||
| 10 | GLU | ASP | ILE | HIS | GLN | TYR | ARG | GLU | GLN | ILE | ||||
| 11 | LYS | ARG | VAL | LYS | ASP | SER | ASP | ASP | VAL | PRO | ||||
| 12 | MET | VAL | LEU | VAL | GLY | ASN | LYS | CYS | ASP | LEU | ||||
| 13 | ALA | 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