6BVM: Ras:SOS:Ras

Ras:SOS:Ras in complex with a small molecule activator. Determined by X-ray diffraction at 1.8 Å resolution. Released 24 Oct 2018.

Method: X-ray diffraction
Resolution: 1.8 Å
Organism: Homo sapiens
Chains: 3
Atoms: 8,096
Mol. weight: 95.87 kDa
Ligands: EBV, MG, GNP
Released: 24 Oct 2018

Explore 6BVM in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6BVM contains 51 α-helices and 18 β-strands across 3 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 7 helices, 6 β-strands

Element	Residues	Length	Sheet
β-strand	2-10	9	1
α-helix	16-25	10
β-strand	37-46	10	1
β-strand	49-58	10	1
α-helix	62-64	3
α-helix	69-74	6
β-strand	77-83	7	1
α-helix	87-91	5
α-helix	93-104	12
β-strand	111-116	6	1
α-helix	127-137	11
β-strand	141-143	3	1
α-helix	152-165	14

Chain B: 36 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	566-568	3
α-helix	576-578	3
α-helix	580-581	2
β-strand	586-588	3	2
β-strand	601-604	4	2
α-helix	606-613	8
α-helix	621-630	10
α-helix	631-633	3
α-helix	637-648	12
α-helix	650-655	6
α-helix	657-664	8
α-helix	667-669	3
α-helix	672-677	6
α-helix	678-682	5
α-helix	683-699	17
α-helix	702-706	5
α-helix	708-719	12
α-helix	727-741	15
α-helix	757-762	6
α-helix	771-773	3
α-helix	781-797	17
α-helix	801-803	3
α-helix	805-810	6
α-helix	814-817	4
α-helix	819-840	22
α-helix	845-864	20
β-strand	867	1	3
α-helix	868-878	11
α-helix	881-884	4
α-helix	887-891	5
α-helix	895-906	12
α-helix	909-919	11
β-strand	927	1	3
α-helix	931-943	13
β-strand	947-950	4	2
β-strand	953-957	5	2
α-helix	958-974	17
α-helix	977-979	3
α-helix	985-992	8
α-helix	1002-1016	15
α-helix	1018-1019	2
α-helix	1023-1025	3

Chain C: 8 helices, 6 β-strands

Element	Residues	Length	Sheet
β-strand	2-10	9	4
α-helix	18-24	7
β-strand	41-46	6	4
β-strand	49-57	9	4
α-helix	65-67	3
α-helix	68-73	6
β-strand	77-83	7	4
α-helix	87-91	5
α-helix	93-104	12
β-strand	111-117	7	4
α-helix	122-123	2
α-helix	127-137	11
β-strand	141-145	5	4
α-helix	152-164	13

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
GTPase HRas	A	protein	167	Homo sapiens	P01112 (AlphaFold model)
Son of sevenless homolog 1	B	protein	482	Homo sapiens	Q07889 (AlphaFold model)
GTPase HRas	C	protein	167	Homo sapiens	P01112 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>6BVM_1 GTPase HRas (chains A)
GMTEYKLVVVGAGGVGKSALTIQLIQNHFVDEYDPTIEDSYRKQVVIDGETCLLDILDTA
GQEEASAMRDQYMRTGEGFLCVFAINNTKSFEDIHQYREQIKRVKDSDDVPMVLVGNKCD
LAARTVESRQAQDLARSYGIPYIETSAKTRQGVEDAFYTLVREIRQH

Sequence of entity 2 (B), FASTA

>6BVM_2 Son of sevenless homolog 1 (chains B)
GQMRLPSADVYRFAEPDSEENIIFEENMQPKAGIPIIKAGTVIKLIERLTYHMYADPNFV
RTFLTTYRSFCKPQELLSLIIERFEIPEPEPTEADRIAIENGDQPLSAELKRFRKEYIQP
VQLRVLNVCRHWVEHHFYDFERDAYLLQRMEEFIGTVRGKAMKKWVESITKIIQRKKIAR
DNGPGHNITFQSSPPTVEWHISRPGHIETFDLLTLHPIEIARQLTLLESDLYRAVQPSEL
VGSVWTKEDKEINSPNLLKMIRHTTNLTLWFEKCIVETENLEERVAVVSRIIEILQVFQE
LNNFNGVLEVVSAMNSSPVYRLDHTFEQIPSRQKKILEEAHELSEDHYKKYLAKLRSINP
PCVPFFGIYLTNILKTEEGNPEVLKRHGKELINFSKRRKVAEITGEIQQYQNQPYCLRVE
SDIKRFFENLNPMGNSMEKEFTDYLFNKSLEIEPRNPKPLPRFPKKYSYPLKSPGVRPSN
PR

Sequence of entity 3 (C), FASTA

>6BVM_3 GTPase HRas (chains C)
GMTEYKLVVVGAGGVGKSALTIQLIQNHFVDEYDPTIEDSYRKQVVIDGETCLLDILDTA
GQEEYSAMRDQYMRTGEGFLCVFAINNTKSFEDIHQYREQIKRVKDSDDVPMVLVGNKCD
LAARTVESRQAQDLARSYGIPYIETSAKTRQGVEDAFYTLVREIRQH

Ligands and cofactors

ID	Name	Formula	Copies
EBV	(2S)-2-amino-1-[(3aR,6aS)-5-[(5-chloro-1H-indol-3-yl)methyl]hexahydropyrrolo[3,…	C26 H28 Cl N5 O	1
MG	Magnesium ion	Mg	1
GNP	Phosphoaminophosphonic acid-guanylate ester	C10 H17 N6 O13 P3	1

Water and common crystallization additives (NA, GOL, FMT) are not listed.

Primary citation

Discovery of Aminopiperidine Indoles That Activate the Guanine Nucleotide Exchange Factor SOS1 and Modulate RAS Signaling. Abbott, J.R., Hodges, T.R., Daniels, R.N. et al. J Med Chem (2018) 61:6002-6017. DOI 10.1021/acs.jmedchem.8b00360 · PubMed

Other PDB entries of the same protein (UniProt P01112 (AlphaFold model), which also has an AlphaFold model), best resolution first:

2CE2 1.0 Å, Crystal structure analysis of a fluorescent form of H-ras P21 in complex with GDP
2EVW 1.05 Å, Crystal structure analysis of a fluorescent form of H-Ras p21 in complex with R-caged GTP
24SQ 1.08 Å, Human HRAS WT (GDP-bound) in complex with macrocyclic peptide inhibitor AP6296
8TBG 1.2 Å, Tricomplex of RMC-7977, HRAS WT, and CypA
2CLD 1.22 Å, Crystal structure analysis of a fluorescent form of H-ras P21 in complex with GDP (2)
2CL6 1.24 Å, Crystal structure analysis of a fluorescent form of H-ras P21 in complex with S-caged GTP
2CL7 1.25 Å, Crystal structure analysis of a fluorescent form of H-ras P21 in complex with GTP
5WDQ 1.25 Å, H-Ras mutant L120A bound to GMP-PNP at 100K
1CTQ 1.26 Å, Structure of P21RAS in complex with gppnhp at 100 K
2CLC 1.3 Å, Crystal structure analysis of a fluorescent form of H-ras P21 in complex with GTP (2)
3K8Y 1.3 Å, Allosteric modulation of H-Ras GTPase
3OIW 1.3 Å, H-RasG12V with allosteric switch in the "on" state

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