1Q11

Crystal structure of an active fragment of human tyrosyl-tRNA synthetase with tyrosinol

Structural Biology Knowledgebase: 1Q11 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.217
  • R-Value Work: 0.197

Literature

Macromolecules
Sequence Display for 1Q11

Classification: LIGASE

Total Structure Weight: 42619.46

Macromolecule Entities
Molecule Chains Length Organism Details
Tyrosyl-tRNA synthetase A 372 Homo sapiens EC#: 6.1.1.1 IUBMB
Fragment: mini TyrRS
Gene Name(s): YARS Gene View
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

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

A 4-[(2S)-2-amino-3-hydroxypropyl]phenol
tyrosinol (Synonym)
C9 H13 N O2
DBLDQZASZZMNSL-QMMMGPOBSA-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)
GOL
Query on GOL

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

A POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.217
  • R-Value Work: 0.197
  • Space Group: P 21 21 2
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 75.82 α = 90.00
b = 162.99 β = 90.00
c = 35.27 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2003-07-18
  • Released Date: 2004-01-06
  • Deposition author(s): Yang, X.-L., Schimmel, P., Ribas de Pouplana, L.

Revision History

  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4
  • 2011-07-13
    Type: Biological assembly | Details: Added software calculated values