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 

wwPDB Validation 3D Report Full Report


This is version 1.2 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

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
ELONGATION FACTOR TU
A
393Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: tufB
Find proteins for P0CE48 (Escherichia coli (strain K12))
Go to UniProtKB:  P0CE48
Entity ID: 2
MoleculeChainsLengthOrganism
TRANSFER-RNA, PHEB77Saccharomyces cerevisiae
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SUC
Query on SUC

Download SDF File 
Download CCD File 
A
SUCROSE
C12 H22 O11
CZMRCDWAGMRECN-UGDNZRGBSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
GNP
Query on GNP

Download SDF File 
Download CCD File 
A
PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
C10 H17 N6 O13 P3
UQABYHGXWYXDTK-UUOKFMHZSA-N
 Ligand Interaction
KIR
Query on KIR

Download SDF File 
Download CCD File 
A
KIRROMYCIN
MOCIMYCIN; DELVOMYCIN; MYC-8003
C43 H60 N2 O12
HMSYAPGFKGSXAJ-PAHGNTJYSA-N
 Ligand Interaction
Modified Residues  11 Unique
IDChainsTypeFormula2D DiagramParent
PHA
Query on PHA
B
L-PEPTIDE LINKINGC9 H11 N OPHE
PSU
Query on PSU
B
RNA LINKINGC9 H13 N2 O9 PU
5MC
Query on 5MC
B
RNA LINKINGC10 H16 N3 O8 PC
M2G
Query on M2G
B
RNA LINKINGC12 H18 N5 O8 PG
1MA
Query on 1MA
B
RNA LINKINGC11 H16 N5 O7 PA
OMC
Query on OMC
B
RNA LINKINGC10 H16 N3 O8 PC
2MG
Query on 2MG
B
RNA LINKINGC11 H16 N5 O8 PG
OMG
Query on OMG
B
RNA LINKINGC11 H16 N5 O8 PG
7MG
Query on 7MG
B
RNA LINKINGC11 H18 N5 O8 PG
YG
Query on YG
B
RNA LINKINGC21 H29 N6 O12 PG
H2U
Query on H2U
B
RNA LINKINGC9 H15 N2 O9 PU
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.35 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.220 
  • Space Group: P 41 3 2
Unit Cell:
Length (Å)Angle (°)
a = 196.410α = 90.00
b = 196.410β = 90.00
c = 196.410γ = 90.00
Software Package:
Software NamePurpose
AMoREphasing
Agrovatadata scaling
DENZOdata reduction
CNSrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2004-05-27
    Type: Initial release
  • Version 1.1: 2012-11-14
    Type: Database references, Derived calculations, Non-polymer description, Other, Refinement description, Structure summary, Version format compliance
  • Version 1.2: 2015-08-19
    Type: Atomic model, Derived calculations, Non-polymer description, Other, Structure summary