2ZJZ | pdb_00002zjz

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

PDB DOI: https://doi.org/10.2210/pdb2ZJZ/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: 2.60 Å
R-Value Free:
0.282 (Depositor), 0.270 (DCC)
R-Value Work:
0.221 (Depositor), 0.210 (DCC)
R-Value Observed:
0.221 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

How GPCRs activate G proteins: Structural changes from 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: 81.93 kDa
Atom Count: 5,028
Modelled Residue Count: 622
Deposited Residue Count: 712
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Guanine nucleotide-binding protein G(i), alpha-1 subunit	A, B	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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P10824
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 1 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] SDF format, chain D [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth B]	C [auth A], D [auth B]	GUANOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₁ P₂ QGWNDRXFNXRZMB-UUOKFMHZSA-N		Interactions Focus chain C [auth A] Focus chain D [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.60 Å
R-Value Free: 0.282 (Depositor), 0.270 (DCC)
R-Value Work: 0.221 (Depositor), 0.210 (DCC)
R-Value Observed: 0.221 (Depositor)

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 101.38	α = 90
b = 164.07	β = 90
c = 53.41	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

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: 2023-11-01
Changes: Data collection, Refinement description
Version 1.4: 2024-11-06
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.