1OB2

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

Structural Biology Knowledgebase: 1OB2 SBKB.org


Experimental Data Snapshot

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

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 1OB2

Classification: HYDROLASE / NUCLEAR PROTEIN

Total Structure Weight: 69916.94


Macromolecule Entities
Molecule Chains Length Organism Details
ELONGATION FACTOR TU A 393 Escherichia coli EC#: 3.6.5.3 IUBMB
Mutation: S1A
Gene Name(s): tufB b3980 JW3943
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Macromolecule Entities
Molecule Chains Length Organism Details
TRANSFER-RNA, PHE B 77 Saccharomyces cerevisiae AMINO-ACYLATED (PHE) AT THE 3' END

Small Molecules
Ligands 4 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
KIR
Query on KIR

A KIRROMYCIN
MOCIMYCIN; DELVOMYCIN; MYC-8003 (Synonym)
C43 H60 N2 O12
HMSYAPGFKGSXAJ-PAHGNTJYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
GNP
Query on GNP

A PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
C10 H17 N6 O13 P3
UQABYHGXWYXDTK-UUOKFMHZSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
SUC
Query on SUC

A SUCROSE
C12 H22 O11
CZMRCDWAGMRECN-UGDNZRGBSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MG
Query on MG

A MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
Modified Residues 11 Unique
ID Chains Type Formula 2D Diagram Parent
2MG
Query on 2MG
B RNA LINKING C11 H16 N5 O8 P G
H2U
Query on H2U
B RNA LINKING C9 H15 N2 O9 P U
M2G
Query on M2G
B RNA LINKING C12 H18 N5 O8 P G
OMC
Query on OMC
B RNA LINKING C10 H16 N3 O8 P C
OMG
Query on OMG
B RNA LINKING C11 H16 N5 O8 P G
YG
Query on YG
B RNA LINKING C21 H29 N6 O12 P G
PSU
Query on PSU
B RNA LINKING C9 H13 N2 O9 P U
5MC
Query on 5MC
B RNA LINKING C10 H16 N3 O8 P C
7MG
Query on 7MG
B RNA LINKING C11 H18 N5 O8 P G
1MA
Query on 1MA
B RNA LINKING C11 H16 N5 O7 P A
PHA
Query on PHA
B L-PEPTIDE LINKING C9 H11 N O PHE

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
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 196.41 α = 90.00
b = 196.41 β = 90.00
c = 196.41 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2003-01-24
  • Released Date: 2004-05-27
  • Deposition author(s): Kristensen, O., Nissen, P., Nyborg, J.

Revision History

  • 2015-08-19
    Type: Linkage | Details: LINK
  • 2015-08-19
    Type: Polymer description | Details: SEQRES
  • 2015-08-19
    Type: Non-polymer description | Details: FORMUL, HETNAM, HET
  • 2015-08-19
    Type: Other | Details: MODRES
  • 2015-08-19
    Type: Atom nomenclature | Details: HETATM
  • 2012-11-14
    Type: Version format compliance | Details: REMARK 4
  • 2012-11-14
    Type: Other | Details: MODRES
  • 2012-11-14
    Type: Biological assembly | Details: REMARK 300,REMARK 350
  • 2012-11-14
    Type: Refinement description | Details: REMARK 3
  • 2012-11-14
    Type: Geometry validation | Details: REMARK 500
  • 2012-11-14
    Type: Sequence database correspondence | Details: SEQADV,DBREF
  • 2012-11-14
    Type: Non-polymer description | Details: HETSYN,FORMUL
  • 2012-11-14
    Type: Polymer description | Details: COMPND