1OB5

T. aquaticus elongation factor EF-Tu complexed with the antibiotic enacyloxin IIa, a GTP analog, and Phe-tRNA

Structural Biology Knowledgebase: 1OB5 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.1 Å
  • R-Value Free: 0.294
  • R-Value Work: 0.280

Literature

Macromolecules
Sequence Display for 1OB5

Classification: HYDROLASE

Total Structure Weight: 213957.73


Macromolecule Entities
Molecule Chains Length Organism Details
ELONGATION FACTOR TU A, C, E 405 Thermus aquaticus EC#: 3.6.5.3 IUBMB
Gene Name(s): tuf tufA
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Macromolecule Entities
Molecule Chains Length Organism Details
TRANSFER-RNA, PHE B, D, F 78 Saccharomyces cerevisiae AMINO-ACYLATED (PHE) AT THE 3' END

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

A, C, E ENACYLOXIN IIA
C33 H45 Cl2 N O11
IWBADCVFZDCUTN-OCXJTLLTSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
GNP
Query on GNP

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

A, C, E MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
Modified Residues 12 Unique
ID Chains Type Formula 2D Diagram Parent
2MG
Query on 2MG
B, D, F RNA LINKING C11 H16 N5 O8 P G
H2U
Query on H2U
B, D, F RNA LINKING C9 H15 N2 O9 P U
M2G
Query on M2G
B, D, F RNA LINKING C12 H18 N5 O8 P G
OMC
Query on OMC
B, D, F RNA LINKING C10 H16 N3 O8 P C
OMG
Query on OMG
B, D, F RNA LINKING C11 H16 N5 O8 P G
YG
Query on YG
B, D, F RNA LINKING C21 H29 N6 O12 P G
PSU
Query on PSU
B, D, F RNA LINKING C9 H13 N2 O9 P U
5MC
Query on 5MC
B, D, F RNA LINKING C10 H16 N3 O8 P C
7MG
Query on 7MG
B, D, F RNA LINKING C11 H18 N5 O8 P G
5MU
Query on 5MU
B, D, F RNA LINKING C10 H15 N2 O9 P U
1MA
Query on 1MA
B, D, F RNA LINKING C11 H16 N5 O7 P A
PHA
Query on PHA
B, D, F L-PEPTIDE LINKING C9 H11 N O PHE

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.1 Å
  • R-Value Free: 0.294
  • R-Value Work: 0.280
  • Space Group: C 1 2 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 212.57 α = 90.00
b = 122.33 β = 121.30
c = 135.68 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2003-01-24
  • Released Date: 2005-10-13
  • Deposition author(s): Dahlberg, C., Nielsen, R.C., Parmeggiani, A., Nyborg, J., Nissen, P.

Revision History

  • 2015-08-19
    Type: Atom nomenclature | Details: HETATM
  • 2015-08-19
    Type: Other | Details: MODRES
  • 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: Version format compliance | Details: REMARK 4
  • 2015-08-19
    Type: Geometry validation | Details: REMARK 500