8GI3 | pdb_00008gi3

Crystal structure of RhoA mutant L69P complexed with GDP

PDB DOI: https://doi.org/10.2210/pdb8GI3/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: 1.52 Å
R-Value Free:
0.209 (Depositor), 0.222 (DCC)
R-Value Work:
0.171 (Depositor), 0.185 (DCC)
R-Value Observed:
0.172 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

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Literature

Ras-like GTPases mutants structure

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

To be published.

Macromolecule Content

Total Structure Weight: 22.52 kDa
Atom Count: 1,640
Modeled Residue Count: 179
Deposited Residue Count: 196
Unique protein chains: 1

Macromolecules

Find similar proteins by:

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) Explore P61586 Go to UniProtKB: P61586
PHAROS: P61586 GTEx: ENSG00000067560
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P61586
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] Interactions & Density 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] Interactions & Density Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.52 Å
R-Value Free: 0.209 (Depositor), 0.222 (DCC)
R-Value Work: 0.171 (Depositor), 0.185 (DCC)
R-Value Observed: 0.172 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 32.048	α = 90
b = 64.081	β = 90
c = 82.504	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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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

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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.