6V9O | pdb_00006v9o

Expanding the Chemical Landscape of SOS1 Activators Using Fragment Based Methods

• PDB DOI: https://doi.org/10.2210/pdb6V9O/pdb

• Classification: SIGNALING PROTEIN
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2019-12-13 Released: 2020-12-16 
• Deposition Author(s): Phan, J., Fesik, S.W.
• Funding Organization(s): Lustgarten Foundation

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.169 (Depositor), 0.170 (DCC) 
• R-Value Work: 
  0.157 (Depositor), 0.160 (DCC) 
• R-Value Observed: 
  0.157 (Depositor) 

Starting Model: experimental

Literature

Expanding the Chemical Landscape of SOS1 Activators Using Fragment Based Methods

Phan, J., Fesik, S.W.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A2B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 96.05 kDa 
• Atom Count: 8,059 
• Modeled Residue Count: 802 
• Deposited Residue Count: 816 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
GTPase HRas	A	167	Homo sapiens	Mutation(s): 0  Gene Names: HRAS, HRAS1 EC: 3.6.5.2
UniProt & NIH Common Fund Data Resources
Find proteins for P01112 (Homo sapiens) Explore P01112  Go to UniProtKB:  P01112
PHAROS:  P01112 GTEx:  ENSG00000174775

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Son of sevenless homolog 1	B	482	Homo sapiens	Mutation(s): 0  Gene Names: SOS1
UniProt & NIH Common Fund Data Resources
Find proteins for Q07889 (Homo sapiens) Explore Q07889  Go to UniProtKB:  Q07889
PHAROS:  Q07889 GTEx:  ENSG00000115904

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
GTPase HRas	C	167	Homo sapiens	Mutation(s): 0  Gene Names: HRAS, HRAS1 EC: 3.6.5.2
UniProt & NIH Common Fund Data Resources
Find proteins for P01112 (Homo sapiens) Explore P01112  Go to UniProtKB:  P01112
PHAROS:  P01112 GTEx:  ENSG00000174775

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GNP	D [auth A]	PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER C10 H17 N6 O13 P3 UQABYHGXWYXDTK-UUOKFMHZSA-N
QTA (Subject of Investigation/LOI)	F [auth B], G [auth B]	3-(phenylsulfonyl)benzene-1-sulfonamide C12 H11 N O4 S2 XYMATFXFXPYYNY-UHFFFAOYSA-N
GOL	M [auth B], N [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
FMT	H [auth B], I [auth B], J [auth B], K [auth B], L [auth B], O [auth B], P [auth C]	FORMIC ACID C H2 O2 BDAGIHXWWSANSR-UHFFFAOYSA-N
MG	E [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N
NA	Q [auth C]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CSO	A	L-PEPTIDE LINKING	C3 H7 N O3 S		CYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.169 (Depositor), 0.170 (DCC) 
• R-Value Work:  0.157 (Depositor), 0.160 (DCC) 
• R-Value Observed: 0.157 (Depositor) 

Space Group: I 4 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 184.144	α = 90
b = 184.144	β = 90
c = 178.865	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data reduction
SCALEPACK	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2020-12-16 
Deposition Author(s): Phan, J., Fesik, S.W.

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Funding Organization	Location	Grant Number
Lustgarten Foundation	United States	--

Revision History  

• Version 1.0: 2020-12-16
  Type: Initial release
  
• Version 1.1: 2023-10-11
  Changes: Data collection, Database references, Refinement description
• Version 1.2: 2023-11-15
  Changes: Data collection
• Version 1.3: 2024-11-06
  Changes: Structure summary