4L87

Crystal structure of the human seryl-tRNA synthetase in complex with Ser-SA at 2.9 Angstrom resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.268
  • R-Value Work: 0.255

Literature

Macromolecules
Sequence Display for 4L87

Classification: LIGASE

Total Structure Weight: 55094.23

Macromolecule Entities
Molecule Chains Length Organism Details
Serine--tRNA ligase, cytoplasmic A 476 Homo sapiens EC#: 6.1.1.11 IUBMB
Fragment: UNP residues 2-477
Gene Name(s): SARS Gene View SERS
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

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

A 5'-O-(N-(L-SERYL)-SULFAMOYL)ADENOSINE
C13 H19 N7 O8 S
HQXFJGONGJPTLZ-YTMOPEAISA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
PO4
Query on PO4

A PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
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: 2.9 Å
  • R-Value Free: 0.268
  • R-Value Work: 0.255
  • Space Group: P 3 2 1

Unit Cell:

Length (Å) Angle (°)
a = 167.07 α = 90.00
b = 167.07 β = 90.00
c = 65.16 γ = 120.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2013-06-16
  • Released Date: 2013-10-02
  • Deposition author(s): Xu, X., Yang, X.-L.

Revision History

  • Version 1_0: 2013-10-02

    Type: Initial release

  • Version 1_1: 2013-11-06

    Type: Database references

  • Version 1_2: 2013-11-27

    Type: Database references

  • Version 1_3: 2017-11-15

    Type: Refinement description