BMRB: 36166

Solution structure of H-RasT35S mutant protein in complex with KBFM123

Authors

Matsumoto, S., Hayashi, Y., Hiraga, T., Matsuo, K., Kataoka, T.

Assembly

GTPase HRas

Entity

1. GTPase HRas (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. PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER (non-polymer), 522.196 Da
3. 3-oxidanyl-~{N}-[[(2~{S})-oxolan-2-yl]methyl]naphthalene-2-carboxamide (non-polymer), 271.311 Da
4. MAGNESIUM ION (non-polymer), 24.305 Da

Total weight

19656.771 Da

Max. entity weight

18838.96 Da

Entity Connection

metal coordination 3 Detail

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ID	Type	Value order	Atom ID 1	Atom ID 2
1	metal coordination	sing	1:SER17:OG	4:MG1:MG
2	metal coordination	sing	2:GNP1:O1G	4:MG1:MG
3	metal coordination	sing	2:GNP1:O2B	4:MG1:MG

Source organism

Homo sapiens

Exptl. method

solution NMR

Refine. method

simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 5.4 %, Completeness: 1.8 %, Completeness (bb): 1.8 % Detail

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Polymer type: polypeptide(L)

	Total	1H	13C
All	1.8 % (32 of 1736)	1.8 % (18 of 992)	1.9 % (14 of 744)
Backbone	1.8 % (15 of 827)	1.8 % (6 of 340)	1.8 % (9 of 487)
Sidechain	1.8 % (19 of 1064)	1.8 % (12 of 652)	1.7 % (7 of 412)
Aromatic	0.0 % (0 of 134)	0.0 % (0 of 67)	0.0 % (0 of 67)
Methyl	4.7 % (9 of 190)	6.3 % (6 of 95)	3.2 % (3 of 95)

1. GTPase HRas

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

Show sample condition

Sample

Solvent system 80% D2O/20% d6-DMSO, Pressure 1 atm, Temperature 278 K, pH 6.8, Details 0.8 mM [U-99% 13C; U-99% 15N] H-RasT35S, 3.0 mM KBFM123, 20 mM sodium phosphate, 40 mM sodium chloride, 8 mM MAGNESIUM ION, 0.8 mM PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER, 80% D2O/20% d6-DMSO

#	Name	Isotope labeling	Type	Concentration
1	H-RasT35S	[U-99% 13C; U-99% 15N]	protein	0.8 mM
2	KBFM123	natural abundance		3.0 mM
3	MAGNESIUM ION	natural abundance		8 mM
4	PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER	natural abundance		0.8 mM
5	sodium chloride	natural abundance	salt	40 mM
6	sodium phosphate	natural abundance	buffer	20 mM
7	D2O	[U-2H]	solvent	80 %
8	d6-DMSO	[U-2H]	solvent	20 %

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Protein Blocks Logo

Calculated from 15 models in PDB: 5ZC6, Strand ID: A Detail

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Release date

2018-09-30

Citation

Molecular Basis for Allosteric Inhibition of GTP-Bound H-Ras Protein by a Small-Molecule Compound Carrying a Naphthalene Ring
Matsumoto, S., Hiraga, T., Hayashi, Y., Yoshikawa, Y., Tsuda, C., Araki, M., Neya, M., Shima, F., Kataoka, T.
Biochemistry (2018), 57, PubMed 30141910 , DOI 10.1021/acs.biochem.8b00680 , Abstract

Related entities 1. GTPase HRas, : 1 : 7 : 96 : 195 entities Detail

Interaction partners 1. GTPase HRas, : 60 interactors Detail

Experiments performed 3 experiments Detail