3MSX | pdb_00003msx

Crystal structure of RhoA.GDP.MgF3 in complex with GAP domain of ArhGAP20

PDB DOI: https://doi.org/10.2210/pdb3MSX/pdb

Classification: PROTEIN BINDING
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2010-04-29 Released: 2011-03-16
Deposition Author(s): Utepbergenov, D., Cooper, D.R., Derewenda, U., Derewenda, Z.S.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.65 Å
R-Value Free:
0.219 (Depositor), 0.219 (DCC)
R-Value Work:
0.195 (Depositor), 0.196 (DCC)
R-Value Observed:
0.196 (Depositor)

wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment

This is version 1.4 of the entry. See complete history.

Literature

Mechanism of molecular specificity of RhoGAP domains towards small GTPases of RhoA family.

Utepbergenov, D., Cooper, D.R., Derewenda, U., Somlyo, A.V., Derewenda, Z.S.

To be published.

Macromolecule Content

Total Structure Weight: 43.49 kDa
Atom Count: 3,193
Modeled Residue Count: 369
Deposited Residue Count: 381
Unique protein chains: 2

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Transforming protein RhoA	A	180	Homo sapiens	Mutation(s): 1 Gene Names: ARH12, ARHA, RHO12, RHOA 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

Find similar proteins by:

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Rho GTPase-activating protein 20	B	201	Homo sapiens	Mutation(s): 0 Gene Names: ARHGAP20, KIAA1391
UniProt & NIH Common Fund Data Resources
Find proteins for Q9P2F6 (Homo sapiens) Explore Q9P2F6 Go to UniProtKB: Q9P2F6
PHAROS: Q9P2F6 GTEx: ENSG00000137727
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9P2F6
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GDP Query on GDP 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]	GUANOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₁ P₂ QGWNDRXFNXRZMB-UUOKFMHZSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
MGF Query on MGF Download:Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A] mmCIF format, chain E [auth A]	E [auth A]	TRIFLUOROMAGNESATE F₃ Mg GJOMWUHGUQLOAC-UHFFFAOYSA-K		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]
MG Query on MG 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]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.65 Å
R-Value Free: 0.219 (Depositor), 0.219 (DCC)
R-Value Work: 0.195 (Depositor), 0.196 (DCC)
R-Value Observed: 0.196 (Depositor)

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 69.057	α = 90
b = 88.977	β = 90
c = 137.725	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
SERGUI	data collection

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2011-03-16

Deposition Author(s):

Utepbergenov, D.

Derewenda, Z.S.

Revision History (Full details and data files)

Version 1.0: 2011-03-16
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2017-11-08
Changes: Refinement description
Version 1.3: 2021-10-06
Changes: Database references, Derived calculations
Version 1.4: 2024-02-21
Changes: Data collection

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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.