2ZJY | pdb_00002zjy

Structure of the K349P mutant of Gi alpha 1 subunit bound to ALF4 and GDP

PDB DOI: https://doi.org/10.2210/pdb2ZJY/pdb

Classification: HYDROLASE
Organism(s): Rattus norvegicus
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2008-03-11 Released: 2009-03-24
Deposition Author(s): Morikawa, T., Muroya, A., Sugio, S., Wakamatsu, K., Kohno, T.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.80 Å
R-Value Free:
0.260 (Depositor), 0.253 (DCC)
R-Value Work:
0.181 (Depositor), 0.173 (DCC)
R-Value Observed:
0.181 (Depositor)

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Ligand Structure Quality Assessment

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Literature

How GPCRs activate G proteins: Structural changes form C-terminal tail to GDP binding pocket

Morikawa, T., Muroya, A., Sugio, S., Wakamatsu, K., Kohno, T.

To be published.

Macromolecule Content

Total Structure Weight: 41.09 kDa
Atom Count: 2,678
Modeled Residue Count: 317
Deposited Residue Count: 356
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Guanine nucleotide-binding protein G(i), alpha-1 subunit	A	356	Rattus norvegicus	Mutation(s): 1 Gene Names: Gnai1, Gnai-1 EC: 3.6.5.1 (PDB Primary Data), 3.6.5 (UniProt)
UniProt
Find proteins for P10824 (Rattus norvegicus) Explore P10824 Go to UniProtKB: P10824
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P10824
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 D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	GUANOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₁ P₂ QGWNDRXFNXRZMB-UUOKFMHZSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]
ALF Query on ALF 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]	TETRAFLUOROALUMINATE ION Al F₄ UYOMQIYKOOHAMK-UHFFFAOYSA-J		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
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: 2.80 Å
R-Value Free: 0.260 (Depositor), 0.253 (DCC)
R-Value Work: 0.181 (Depositor), 0.173 (DCC)
R-Value Observed: 0.181 (Depositor)

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 79.375	α = 90
b = 79.375	β = 90
c = 105.297	γ = 120

Software Package:

Software Name	Purpose
CNS	refinement
CrystalClear	data collection
DENZO	data reduction
SCALEPACK	data scaling
CNS	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2009-03-24

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2009-03-24
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2021-11-10
Changes: Database references, Derived calculations
Version 1.3: 2024-05-29
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.