1NJ5

Crystal structure of Prolyl-tRNA Synthetase from Methanothermobacter thermautotrophicus bound to proline sulfamoyl adenylate

Structural Biology Knowledgebase: 1NJ5 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.254
  • R-Value Work: 0.222

Literature

Macromolecules
Sequence Display for 1NJ5

Classification: LIGASE

Total Structure Weight: 58703.97

Macromolecule Entities
Molecule Chains Length Organism Details
Proline-tRNA Synthetase A 501 Methanothermobacter thermautotrophicus EC#: 6.1.1.15 IUBMB
Fragment: N terminally His Tagged Enzyme
Mutation: T473Y, G474R, L475A, T476Y, P478A, E479R, H480T, I481Y
Gene Name(s): proS MTH_611
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 3 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
P5A
Query on P5A

A '5'-O-(N-(L-PROLYL)-SULFAMOYL)ADENOSINE
C15 H21 N7 O7 S
LKVJEMXWEODCAY-JVEUSOJLSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
ZN
Query on ZN

A ZINC ION
Zn
PTFCDOFLOPIGGS-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)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
P5A N/A in BindingDB
N/A in BindingMoad
Ki: 50 nM  PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.254
  • R-Value Work: 0.222
  • Space Group: P 65 2 2
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 143.96 α = 90.00
b = 143.96 β = 90.00
c = 163.94 γ = 120.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2002-12-30
  • Released Date: 2003-03-04
  • Deposition author(s): Kamtekar, S., Kennedy, W.D., Wang, J., Stathopoulos, C., Soll, D., Steitz, T.A.

Revision History

  • 2011-07-13
    Type: Biological assembly | Details: Added software calculated values
  • 2011-07-13
    Type: Source and taxonomy | Details: Removed strain from scientific name
  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4