8GI6

Crystal structure of RhoA mutant L69R complexed with GDP

PDB DOI: https://doi.org/10.2210/pdb8GI6/pdb

Classification: HYDROLASE
Organism(s): Homo sapiens
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2023-03-13 Released: 2024-03-20
Deposition Author(s): Chen, X., Qian, X., Chandravanshi, M., Lowy, D.R., Walters, K.J.
Funding Organization(s): National Institutes of Health/National Cancer Institute (NIH/NCI)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.40 Å
R-Value Free: 0.182
R-Value Work: 0.153
R-Value Observed: 0.154

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Ras-like GTPases mutant structures

Chen, X., Qian, X., Chandravanshi, M., Lowy, D.R., Walters, K.J.

To be published.

Macromolecule Content

Total Structure Weight: 22.58 kDa
Atom Count: 1,640
Modelled Residue Count: 178
Deposited Residue Count: 196
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Transforming protein RhoA	A	196	Homo sapiens	Mutation(s): 1 Gene Names: RHOA, ARH12, ARHA, RHO12 EC: 3.6.5.2
UniProt & NIH Common Fund Data Resources
Find proteins for P61586 (Homo sapiens) Go to UniProtKB: P61586
PHAROS: P61586 GTEx: ENSG00000067560
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GDP (Subject of Investigation/LOI) Query on GDP Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	GUANOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₁ P₂ QGWNDRXFNXRZMB-UUOKFMHZSA-N		Interactions Focus chain B [auth A]
MG (Subject of Investigation/LOI) 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]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.40 Å
R-Value Free: 0.182
R-Value Work: 0.153
R-Value Observed: 0.154
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 31.96	α = 90
b = 64.187	β = 90
c = 83.078	γ = 90

Software Package:

Software Name	Purpose
SERGUI	data collection
MOLREP	phasing
REFMAC	refinement
Coot	model building
PDB_EXTRACT	data extraction
DIALS	data reduction
Aimless	data scaling

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2024-03-20

Deposition Author(s):

Chandravanshi, M.

Funding Organization	Location	Grant Number
National Institutes of Health/National Cancer Institute (NIH/NCI)	United States	1 ZIA BC011490

Revision History (Full details and data files)

Version 1.0: 2024-03-20
Type: Initial release
Version 1.1: 2024-04-03
Changes: Structure summary

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.