5MLA

Crystal structure of human RAS in complex with darpin K55

• PDB DOI: https://doi.org/10.2210/pdb5MLA/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens, synthetic construct
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2016-12-06 Released: 2017-12-20 
• Deposition Author(s): Debreczeni, J.E., Guillard, S., Kolasinska-Zwierz, P., Breed, J., Zhang, J., Bery, N., Marwood, R., Tart, J., Overman, R., Stocki, P., Mistry, B., Phillips, C., Rabbitts, T., Jackson, R., Minter, R.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.19 Å
• R-Value Free: 
  0.229 (Depositor), 0.230 (DCC) 
• R-Value Work: 
  0.182 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.184 (Depositor) 

Literature

Inhibition of RAS nucleotide exchange by a DARPin: structural characterisation and effects on downstream signalling by active RAS

Guillard, S., Kolasinska-Zwierz, P., Debreczeni, J., Breed, J., Zhang, J., Bery, N., Marwood, R., Tart, J., Overman, R., Stocki, P., Minstry, B., Phillips, C., Rabbitts, T., Jackson, R., Minter, R.

To be published.

Biological Assembly 1  

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

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

Macromolecule Content

• Total Structure Weight: 40.41 kDa 
• Atom Count: 2,449 
• Modelled Residue Count: 306 
• Deposited Residue Count: 356 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
GTPase KRas	A	169	Homo sapiens	Mutation(s): 1  Gene Names: KRAS, KRAS2, RASK2 EC: 3.6.5.2
UniProt & NIH Common Fund Data Resources
Find proteins for P01116 (Homo sapiens) Explore P01116  Go to UniProtKB:  P01116
PHAROS:  P01116 GTEx:  ENSG00000133703

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
darpin k55	B	187	synthetic construct	Mutation(s): 0

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GSP	D [auth A]	5'-GUANOSINE-DIPHOSPHATE-MONOTHIOPHOSPHATE C10 H16 N5 O13 P3 S XOFLBQFBSOEHOG-UUOKFMHZSA-N
SO4	E [auth A], F [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
MG	C [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.19 Å
• R-Value Free:  0.229 (Depositor), 0.230 (DCC) 
• R-Value Work:  0.182 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.184 (Depositor) 

Space Group: H 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 112.83	α = 90
b = 112.83	β = 90
c = 66.77	γ = 120

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-12-20 
Deposition Author(s): Debreczeni, J.E., Guillard, S., Kolasinska-Zwierz, P., Breed, J., Zhang, J., Bery, N., Marwood, R., Tart, J., Overman, R., Stocki, P., Mistry, B., Phillips, C., Rabbitts, T., Jackson, R., Minter, R.

Revision History  

• Version 1.0: 2017-12-20
  Type: Initial release
  
• Version 1.1: 2024-05-08
  Changes: Data collection, Database references, Derived calculations