3VQX

Crystal structure of the catalytic domain of pyrrolysyl-tRNA synthetase in triclinic crystal form

Structural Biology Knowledgebase: 3VQX SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.270
  • R-Value Work: 0.212

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 3VQX

Classification: LIGASE

Total Structure Weight: 135602.98

Macromolecule Entities
Molecule Chains Length Organism Details
Pyrrolysine--tRNA ligase A, B, C, D 291 Methanosarcina mazei EC#: 6.1.1.26 IUBMB
Gene Name(s): pylS MM_1445
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

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

C, D [[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4- bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl- phosphoryl] (2S)-2-azanyl-6-[(2-methylpropan- 2-yl)oxycarbonylamino]hexanoate
C21 H34 N7 O10 P
XYDQQGDGPLGSGU-URQYDQELSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
AMP
Query on AMP

A, B ADENOSINE MONOPHOSPHATE
C10 H14 N5 O7 P
UDMBCSSLTHHNCD-KQYNXXCUSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
PO4
Query on PO4

A, B, C, D PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.270
  • R-Value Work: 0.212
  • Space Group: P 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 62.80 α = 106.92
b = 69.42 β = 91.41
c = 83.33 γ = 113.83

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2012-04-02
  • Released Date: 2013-01-02
  • Deposition author(s): Yanagisawa, T., Sumida, T., Ishii, R., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Revision History

  • 2013-09-04
    Type: Citation | Details: Citation update