5MLA | pdb_00005mla

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.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.19 Å
R-Value Free:
0.229 (Depositor), 0.231 (DCC)
R-Value Work:
0.182 (Depositor), 0.188 (DCC)
R-Value Observed:
0.184 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 5MLA

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

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.

Macromolecule Content

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

Macromolecules

Find similar proteins by:

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 Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P01116
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

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	3D Interactions
GSP Query on GSP Download:Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	5'-GUANOSINE-DIPHOSPHATE-MONOTHIOPHOSPHATE C₁₀ H₁₆ N₅ O₁₃ P₃ S XOFLBQFBSOEHOG-UUOKFMHZSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth B] MOL2 format, chain E [auth A] MOL2 format, chain F [auth B] mmCIF format, chain E [auth A] mmCIF format, chain F [auth B]	E [auth A], F [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain E [auth A] Focus chain F [auth B] Interactions & Density Focus chain E [auth A] Focus chain F [auth B]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.19 Å
R-Value Free: 0.229 (Depositor), 0.231 (DCC)
R-Value Work: 0.182 (Depositor), 0.188 (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

View Full Validation Report

Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2017-12-20

Deposition Author(s):

Debreczeni, J.E.

Kolasinska-Zwierz, P.

Revision History (Full details and data files)

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

RCSB PDB is hosted by

RCSB PDB is a member of

RCSB Partners
Nucleic Acid Knowledgebase

CoreTrustSeal

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.