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BMRB: 18629

2LWI

Solution structure of H-RasT35S mutant protein in complex with Kobe2601

Authors

Araki, M., Tamura, A.

Assembly

H-RasT35S mutant protein in complex with Kobe2601

Entity

1. H-RasT35S mutant protein in complex with Kobe2601, entity 1 (polymer, Thiol state: all free), 166 monomers, 18838.96 Da Detail

MTEYKLVVVG AGGVGKSALT IQLIQNHFVD EYDPSIEDSY RKQVVIDGET CLLDILDTAG QEEYSAMRDQ YMRTGEGFLC VFAINNTKSF EDIHQYREQI KRVKDSDDVP MVLVGNKCDL AARTVESRQA QDLARSYGIP YIETSAKTRQ GVEDAFYTLV REIRQH

2. 2-(2,4-dinitrophenyl)-N-(4-fluorophenyl)hydrazinecarbothioamide (non-polymer), 351.313 Da
3. PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER (non-polymer), 522.196 Da
4. MAGNESIUM ION (non-polymer), 24.305 Da
5. WATER (water), 18.015 × 3 Da

Total weight

19736.773 Da

Max. entity weight

18838.96 Da

Source organism

Homo sapiens

Exptl. method

solution NMR

Refine. method

simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 38.0 %, Completeness: 13.7 %, Completeness (bb): 6.8 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C
All	13.7 % (237 of 1736)	13.3 % (132 of 992)	14.1 % (105 of 744)
Backbone	6.8 % (56 of 827)	5.9 % (20 of 340)	7.4 % (36 of 487)
Sidechain	18.9 % (201 of 1064)	17.2 % (112 of 652)	21.6 % (89 of 412)
Aromatic	3.0 % (4 of 134)	6.0 % (4 of 67)	0.0 % (0 of 67)
Methyl	75.8 % (144 of 190)	76.8 % (73 of 95)	74.7 % (71 of 95)

1. entity 1

MTEYKLVVVG AGGVGKSALT IQLIQNHFVD EYDPSIEDSY RKQVVIDGET CLLDILDTAG QEEYSAMRDQ YMRTGEGFLC VFAINNTKSF EDIHQYREQI KRVKDSDDVP MVLVGNKCDL AARTVESRQA QDLARSYGIP YIETSAKTRQ GVEDAFYTLV REIRQH

Show sample condition

Sample #1

Solvent system 80% D2O/20% DMSO_d6, Pressure 1 atm, Temperature 278 K, pH 6.8

#	Name	Isotope labeling	Concentration
1	H-RasT35S	[U-98% 13C; U-98% 15N]	1 mM
2	PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER	natural abundance	1 mM
3	MAGNESIUM ION	natural abundance	8 mM
4	sodium chloride	natural abundance	120 mM
5	sodium phosphate	natural abundance	20 mM
6	KOB	natural abundance	3.8 mM
7	D2O	natural abundance	80 %
8	DMSO_d6	natural abundance	20 %

Sample #2

Solvent system 80% D2O/20% DMSO_d6, Pressure 1 atm, Temperature 278 K, pH 6.8

#	Name	Isotope labeling	Concentration
9	H-RasT35S	natural abundance	1 mM
10	PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER	natural abundance	1 mM
11	MAGNESIUM ION	natural abundance	8 mM
12	sodium chloride	natural abundance	120 mM
13	sodium phosphate	natural abundance	20 mM
14	KOB	natural abundance	3.8 mM
15	D2O	natural abundance	80 %
16	DMSO_d6	natural abundance	20 %

Protein Blocks Logo

Calculated from 15 models in PDB: 2LWI, Strand ID: A Detail

Release date

2012-08-29

Citation

In silico discovery of small-molecule Ras inhibitors that display antitumor activity by blocking the Ras-effector interaction
Ye, M., Shima, F., Yoshikawa, Y., Araki, M., Matsumoto, S., Liao, J., Hu, L., Sugimoto, T., Ijiri, Y., Takeda, A., Nishiyama, Y., Sato, C., Muraoka, S., Tamura, A., Osoda, T., Tsuda, K., Miyakawa, T., Fukunishi, H., Shimada, J., Kumasaka, T., Yamamotog, M., Kataoka, T.
Proc. Natl. Acad. Sci. U. S. A. (2013), 110, 8182-8187, PubMed 23630290 , DOI 10.1073/pnas.1217730110 , Abstract

Related entities 1. H-RasT35S mutant protein in complex with Kobe2601, entity 1, : 1 : 7 : 96 : 196 entities Detail

Interaction partners 1. H-RasT35S mutant protein in complex with Kobe2601, entity 1, : 60 interactors Detail

More details for 60 interactors identified by 28 citations

Experiments performed 3 experiments Detail

NMR combined restraints 4 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_18629_2lwi.nef
Input source #2: Coordindates	2lwi.cif
Diamagnetism of the molecular assembly	False (excluding Oxygen atoms)
Whether the assembly has a disulfide bond	None
Whether the assembly has a other bond	True (see coodinates for details)
Whether the assembly contains a cyclic polymer	None
Overall data processing status	Error

Disulfide bonds

None

Other bonds (neither disulfide, covalent nor hydrogen bonds, e.g. Zinc–sulphur bond)

Ptnr_site_1	Ptnr_site_2	Distance (Å)
B:null:GNP:O2G	C:null:MG:MG	2.079
A:23:SER:OG	C:null:MG:MG	2.214
C:null:MG:MG	E:null:HOH:O	2.235
C:null:MG:MG	E:null:HOH:O	2.244
B:null:GNP:O2B	C:null:MG:MG	2.293
C:null:MG:MG	E:null:HOH:O	2.302

Non-standard residues

Chain_ID	Seq_ID	Comp_ID	Chem_comp_name	Experimental evidences
B	1	MG	MAGNESIUM ION	None
C	1	GNP	PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER	None
D	1	KOB	2-(2,4-dinitrophenyl)-N-(4-fluorophenyl)hydrazinecarbothioamide	Assigned chemical shifts

Sequence alignments

Entity_assembly_ID (NMR): A vs Auth_asym_ID (model): A

--------------10--------20--------30--------40--------50--------60--------70--------80--------90----
GPLGSDMTEYKLVVVGAGGVGKSALTIQLIQNHFVDEYDPSIEDSYRKQVVIDGETCLLDILDTAGQEEYSAMRDQYMRTGEGFLCVFAINNTKSFEDIH
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
GPLGSDMTEYKLVVVGAGGVGKSALTIQLIQNHFVDEYDPSIEDSYRKQVVIDGETCLLDILDTAGQEEYSAMRDQYMRTGEGFLCVFAINNTKSFEDIH
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100

---100-------110-------120-------130-------140-------150-------160------
QYREQIKRVKDSDDVPMVLVGNKCDLAARTVESRQAQDLARSYGIPYIETSAKTRQGVEDAFYTLVREIRQH
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
QYREQIKRVKDSDDVPMVLVGNKCDLAARTVESRQAQDLARSYGIPYIETSAKTRQGVEDAFYTLVREIRQH
-------110-------120-------130-------140-------150-------160-------170--

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	172	0	0	100.0

Content subtype: combined_18629_2lwi.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	245		32.6 (chain: A, length: 172), 100.0 (chain: D, length: 1)
1	Distance restraints	DYANA/DIANA_distance_constraints_3	Warning	1700 (1)	noe	96.5 (chain: A, length: 172)
1	Dihedral angle restraints	DYANA/DIANA_dihedral_4	OK	230 (230)	.	80.8 (chain: A, length: 172)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 172, Sequence coverage: 32.6%
  - Entity_assembly_ID: D, Chain length: 1, Sequence coverage: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 168
  - ¹³C chemical shifts: 77
- Completeness of assignments
  - Entity_assemble_ID: D
- Rotameric state of ILE , LEU, and VAL
- Histogram of normalized assigned chemical shifts
- Random coil index and derived parameters (S² and NMR RMSD)
  - Chain_ID: A

Comp_index_ID	Comp_ID
1	KOB

Distance restraints

Saveframe: DYANA/DIANA_distance_constraints_3
- Status: Warning
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 172, Sequence coverage: 96.5%
- Total number of restraints: 1700
- Weight of restraints: 1.0 (1700)
- Potential type of restraints: upper-bound-parabolic (1700)
- Range of distance target values: 2.76, 5.5 (Å)
- Histogram of distance target values
- Distance restraints per residue
  - Chain_ID: A
  - Chain_ID: B
    None
  - Chain_ID: C
    None
  - Chain_ID: D
    None
- Distance restraints on contact map

Dihedral angle restraints

Saveframe: DYANA/DIANA_dihedral_4
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 172, Sequence coverage: 80.8%
- Total number of restraints: 230
- Total number of restraints per polymer type: 230
- Weight of restraints: 1.0 (230)
- Potential type of restraints: square-well-parabolic (230)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords Conformational states, GTP-bound form, Ras, Signaling protein, GTP-Bound Form, Inhibitor, Signaling Protein

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Found 1 Document (2.007 seconds)

BMRB: 18629

Sample #1

Sample #2

Related entities 1. H-RasT35S mutant protein in complex with Kobe2601, entity 1, : 1 : 7 : 96 : 196 entities Detail

Interaction partners 1. H-RasT35S mutant protein in complex with Kobe2601, entity 1, : 60 interactors Detail

Experiments performed 3 experiments Detail

Instrument

Sample

Instrument

Sample

Instrument

Sample

NMR combined restraints 4 contents Detail