5MLB | pdb_00005mlb

Crystal structure of human RAS in complex with darpin K27

• PDB DOI: https://doi.org/10.2210/pdb5MLB/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: 3.22 Å
• R-Value Free: 
  0.235 (Depositor), 0.236 (DCC) 
• R-Value Work: 
  0.201 (Depositor), 0.203 (DCC) 
• R-Value Observed: 
  0.203 (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)

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly 3  

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

Biological assembly 3 assigned by authors and generated by PISA (software)

Biological Assembly 4  

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

Biological assembly 4 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 156.83 kDa 
• Atom Count: 9,902 
• Modeled Residue Count: 1,283 
• Deposited Residue Count: 1,388 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
GTPase KRas	A, C, E, G	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 K27	B, D, F, H	178	synthetic construct	Mutation(s): 0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GDP	I [auth A], K [auth C], M [auth E], O [auth G]	GUANOSINE-5'-DIPHOSPHATE C10 H15 N5 O11 P2 QGWNDRXFNXRZMB-UUOKFMHZSA-N
MG	J [auth A], L [auth C], N [auth E], P [auth G]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.22 Å
• R-Value Free:  0.235 (Depositor), 0.236 (DCC) 
• R-Value Work:  0.201 (Depositor), 0.203 (DCC) 
• R-Value Observed: 0.203 (Depositor) 

Space Group: P 6₅

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 197.14	α = 90
b = 197.14	β = 90
c = 84.61	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, Refinement description