1E22

LYSYL-TRNA SYNTHETASE (LYSU) HEXAGONAL FORM COMPLEXED WITH LYSINE AND THE NON-HYDROLYSABLE ATP ANALOGUE AMP-PCP

Structural Biology Knowledgebase: 1E22 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.43 Å
  • R-Value Free: 0.228
  • R-Value Work: 0.176

Literature

Macromolecules
Sequence Display for 1E22

Classification: LIGASE

Total Structure Weight: 59045.73

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
ACP
Query on ACP

A PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER
ADENOSINE-5'-[BETA, GAMMA-METHYLENE]TRIPHOSPHATE (Synonym)
C11 H18 N5 O12 P3
UFZTZBNSLXELAL-IOSLPCCCSA-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)
MG
Query on MG

A MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.43 Å
  • R-Value Free: 0.228
  • R-Value Work: 0.176
  • Space Group: P 61 2 2
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 142.02 α = 90.00
b = 142.02 β = 90.00
c = 175.39 γ = 120.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2000-05-15
  • Released Date: 2000-07-28
  • Deposition author(s): Desogus, G., Todone, F., Brick, P., Onesti, S.

Revision History

  • 2011-08-24
    Type: Source and taxonomy | Details: SOURCE
  • 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
  • 2011-08-24
    Type: Refinement description | Details: REMARK 3
  • 2011-08-24
    Type: Other | Details: REMARK 465,REMARK 525,MASTER,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