4CH5

Structure of pyrrolysyl-tRNA synthetase in complex with adenylated propionyl lysine

Structural Biology Knowledgebase: 4CH5 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.189
  • R-Value Work: 0.174

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 4CH5

Classification: LIGASE

Total Structure Weight: 34458.54

Macromolecule Entities
Molecule Chains Length Organism Details
PYRROLYSINE--TRNA LIGASE A 291 Methanosarcina mazei EC#: 6.1.1.26 IUBMB
Fragment: CATALYTIC DOMAIN, RESIDUES 185-454
Gene Name(s): pylS MM_1445

Small Molecules
Ligands 4 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
YLP
Query on YLP

A (S)-2-amino-6-propionamidohexanoic(((2R,3S,4R,5R)- 5-(6-amino-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran- 2-yl)methyl phosphoric) anhydride
C19 H30 N7 O9 P
DOJLWXPRSAYJFD-MBRXSIFGSA-M
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
POP
Query on POP

A PYROPHOSPHATE 2-
H2 O7 P2
XPPKVPWEQAFLFU-UHFFFAOYSA-L
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
EDO
Query on EDO

A 1,2-ETHANEDIOL
ETHYLENE GLYCOL (Synonym)
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MG
Query on MG

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

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.189
  • R-Value Work: 0.174
  • Space Group: P 64
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 105.38 α = 90.00
b = 105.38 β = 90.00
c = 70.80 γ = 120.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2013-11-28
  • Released Date: 2014-03-19
  • Deposition author(s): Fluegel, V., Vrabel, M., Schneider, S.

Revision History

  • 2014-05-07
    Type: Citation | Details: JRNL