1E24

LYSYL-TRNA SYNTHETASE (LYSU) HEXAGONAL FORM COMPLEXED WITH LYSINE AND ATP AND MN2+

Structural Biology Knowledgebase: 1E24 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 0.249
  • R-Value Work: 0.182

Literature

Macromolecules
Sequence Display for 1E24

Classification: LIGASE

Total Structure Weight: 58771.22

Macromolecule Entities
Molecule Chains Length Organism Details
LYSYL-TRNA SYNTHETASE A 504 Escherichia coli EC#: 6.1.1.6 IUBMB
Gene Name(s): lysU b4129 JW4090
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

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

A ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
LYS
Query on LYS

A LYSINE
C6 H15 N2 O2
KDXKERNSBIXSRK-YFKPBYRVSA-O
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
GOL
Query on GOL

A GLYCEROL
2, (Synonym)
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MN
Query on MN

A MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 0.249
  • R-Value Work: 0.182
  • Space Group: P 61 2 2
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 143.60 α = 90.00
b = 143.60 β = 90.00
c = 177.23 γ = 120.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2000-05-16
  • Released Date: 2000-07-28
  • Deposition author(s): Desogus, G., Todone, F., Brick, P., Onesti, S.

Revision History

  • 2011-08-24
    Type: Other | Details: REMARK 465,REMARK 525,REMARK 280
  • 2011-08-24
    Type: Atom nomenclature | Details: HETATM
  • 2011-08-24
    Type: Biological assembly | Details: REMARK 300,REMARK 350
  • 2011-08-24
    Type: Linkage | Details: LINK
  • 2011-08-24
    Type: Refinement description | Details: REMARK 3
  • 2011-08-24
    Type: Binding sites and description | Details: REMARK 800,SITE
  • 2011-08-24
    Type: Non-polymer description | Details: HETSYN,FORMUL,REMARK 620,HET
  • 2011-08-24
    Type: Geometry validation | Details: REMARK 500
  • 2011-08-24
    Type: Version format compliance | Details: REMARK 4