1DAR

ELONGATION FACTOR G IN COMPLEX WITH GDP

• PDB DOI: https://doi.org/10.2210/pdb1DAR/pdb

• Classification: TRANSLATIONAL GTPASE
• Organism(s): Thermus thermophilus HB8
• Mutation(s): No 


• Deposited: 1996-02-15 Released: 1996-07-11 
• Deposition Author(s): Al-Karadaghi, S., Aevarsson, A., Garber, M., Zheltonosova, J., Liljas, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.290 
• R-Value Work: 0.220 
• R-Value Observed: 0.220 

Literature

The structure of elongation factor G in complex with GDP: conformational flexibility and nucleotide exchange.

al-Karadaghi, S., Aevarsson, A., Garber, M., Zheltonosova, J., Liljas, A.

(1996) Structure 4: 555-565

• PubMed: 8736554 
• DOI: https://doi.org/10.1016/s0969-2126(96)00061-5
• Primary Citation of Related Structures:  
  1DAR


• PubMed Abstract: 
  

  Elongation factor G (EF-G) catalyzes the translocation step of translation. During translocation EF-G passes through four main conformational states: the GDP complex, the nucleotide-free state, the GTP complex, and the GTPase conformation. The first two of these conformations have been previously investigated by crystallographic methods.

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Organizational Affiliation: 

Department of Molecular Biophysics, Lund University, Sweden.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 77.42 kDa 
• Atom Count: 4,893 
• Modelled Residue Count: 619 
• Deposited Residue Count: 691 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ELONGATION FACTOR G	A	691	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for Q5SHN5 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q5SHN5  Go to UniProtKB:  Q5SHN5

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GDP	B [auth A]	GUANOSINE-5'-DIPHOSPHATE C10 H15 N5 O11 P2 QGWNDRXFNXRZMB-UUOKFMHZSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
GDP	PDBBind:  1DAR	Kd: 1.10e+4 (nM) from 1 assay(s)
	Binding MOAD:  1DAR	Kd: 1.10e+4 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.290 
• R-Value Work: 0.220 
• R-Value Observed: 0.220 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 76.3	α = 90
b = 106.4	β = 90
c = 115.6	γ = 90

Software Package:

Software Name	Purpose
X-PLOR	model building
X-PLOR	refinement
DENZO	data reduction
CCP4	data scaling
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 1996-07-11 
Deposition Author(s): Al-Karadaghi, S., Aevarsson, A., Garber, M., Zheltonosova, J., Liljas, A.

Revision History  

• Version 1.0: 1996-07-11
  Type: Initial release
  
• Version 1.1: 2008-03-24
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Source and taxonomy, Version format compliance
• Version 1.3: 2024-02-07
  Changes: Data collection, Database references, Derived calculations, Other