4NDA

Crystal structure of 3-nitro-tyrosine tRNA synthetase (5B) bound to 3-nitro-tyrosine

Structural Biology Knowledgebase: 4NDA SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.223
  • R-Value Work: 0.180

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 4NDA

Classification: LIGASE

Total Structure Weight: 36521.55

Macromolecule Entities
Molecule Chains Length Organism Details
Tyrosine--tRNA ligase A 314 Methanocaldococcus jannaschii EC#: 6.1.1.1 IUBMB
Mutation: Y32H, H70C, D158S, I159A, L162R
Gene Name(s): tyrS MJ0389

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

A META-NITRO-TYROSINE
C9 H10 N2 O5
FBTSQILOGYXGMD-LURJTMIESA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
GOL
Query on GOL

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

A SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.223
  • R-Value Work: 0.180
  • Space Group: P 43 21 2
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 102.07 α = 90.00
b = 102.07 β = 90.00
c = 71.72 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2013-10-25
  • Released Date: 2014-03-19
  • Deposition author(s): Cooley, R.B., Driggers, C.M., Karplus, P.A., Mehl, R.A.

Revision History

  • 2014-04-16
    Type: Citation | Details: Citation update