1OB2

E. coli elongation factor EF-Tu complexed with the antibiotic kirromycin, a GTP analog, and Phe-tRNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.35 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.220 
  • R-Value Observed: 0.220 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 2.0 of the entry. See complete history


Literature

Kirromycin Defines a Specific Domain Arrangement of Elongation Factor EF-TU

Nielsen, R.C.Kristensen, O.Kjeldgaard, M.Thirup, S.Nissen, P.

To be published.

Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
ELONGATION FACTOR TUA393Escherichia coli BL21Mutation(s): 0 
EC: 3.6.1.48
UniProt
Find proteins for P0CE48 (Escherichia coli (strain K12))
Explore P0CE48 
Go to UniProtKB:  P0CE48
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0CE48
Protein Feature View
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  • Reference Sequence
Find similar nucleic acids by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChainsLengthOrganismImage
TRANSFER-RNA, PHEB 77Saccharomyces cerevisiae
Protein Feature View
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  • Reference Sequence
Oligosaccharides

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Entity ID: 3
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
beta-D-fructofuranose-(2-1)-alpha-D-glucopyranoseC 2N/A Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G05551OP
GlyCosmos:  G05551OP
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
KIR
Query on KIR

Download Ideal Coordinates CCD File 
D [auth A]KIRROMYCIN
C43 H60 N2 O12
HMSYAPGFKGSXAJ-PAHGNTJYSA-N
 Ligand Interaction
GNP
Query on GNP

Download Ideal Coordinates CCD File 
E [auth A]PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
C10 H17 N6 O13 P3
UQABYHGXWYXDTK-UUOKFMHZSA-N
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
F [auth A]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
PHA
Query on PHA
B L-PEPTIDE LINKINGC9 H11 N OPHE
Biologically Interesting Molecules (External Reference) 1 Unique
Entity ID: 3
IDChainsNameType/Class2D Diagram3D Interactions
PRD_900003
Query on PRD_900003
CsucroseOligosaccharide / Nutrient Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.35 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.220 
  • R-Value Observed: 0.220 
  • Space Group: P 41 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 196.41α = 90
b = 196.41β = 90
c = 196.41γ = 90
Software Package:
Software NamePurpose
CNSrefinement
DENZOdata reduction
Agrovatadata scaling
AMoREphasing

Structure Validation

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Ligand Structure Quality Assessment 



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2004-05-27
    Type: Initial release
  • Version 1.1: 2012-11-14
    Changes: Database references, Derived calculations, Non-polymer description, Other, Refinement description, Structure summary, Version format compliance
  • Version 1.2: 2015-08-19
    Changes: Atomic model, Derived calculations, Non-polymer description, Other, Structure summary
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Non-polymer description, Other, Structure summary