8WWC

De novo design binder of HRAS -120-4

• PDB DOI: https://doi.org/10.2210/pdb8WWC/pdb

• Classification: DE NOVO PROTEIN
• Organism(s): synthetic construct, Homo sapiens
• Expression System: Escherichia coli, Escherichia coli 0.1197
• Mutation(s): No 


• Deposited: 2023-10-25 Released: 2024-10-09 
• Deposition Author(s): Wang, L., Wang, S., Liu, Y.
• Funding Organization(s): Not funded

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 0.247 
• R-Value Work: 0.218 
• R-Value Observed: 0.221 

Starting Model: in silico

Literature

De novo design HRAS binder 120-4

Wang, L., Wang, S., Liu, Y.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: isothermal titration calorimetry

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 65.95 kDa 
• Atom Count: 4,060 
• Modelled Residue Count: 553 
• Deposited Residue Count: 572 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
De novo design protein 120-4	A [auth C], D	120	synthetic construct	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
GTPase HRas	B [auth A], C [auth B]	166	Homo sapiens	Mutation(s): 0  Gene Names: HRAS 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 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GNP (Subject of Investigation/LOI)	E [auth A], G [auth B]	PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER C10 H17 N6 O13 P3 UQABYHGXWYXDTK-UUOKFMHZSA-N
MG (Subject of Investigation/LOI)	F [auth A], H [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 0.247 
• R-Value Work: 0.218 
• R-Value Observed: 0.221 
• Space Group: P 6₃

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 89.967	α = 90
b = 89.967	β = 90
c = 188.124	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
Aimless	data scaling
XDS	data reduction
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-10-09 
Deposition Author(s): Wang, L., Wang, S., Liu, Y.

---

Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2024-10-09
  Type: Initial release