3LSS

Trypanosoma brucei seryl-tRNA synthetase in complex with ATP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.195 
  • R-Value Work: 0.168 
  • R-Value Observed: 0.169 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

X-ray crystal structure of Seryl-tRNA synthetase from the eukaryotic parasite Trypanosoma brucei.

Larson, E.T.Zhang, L.Napuli, A.Mueller, N.Verlinde, C.L.M.J.Van Voorhis, W.C.Buckner, F.S.Fan, E.Hol, W.G.J.Merritt, E.A.

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Seryl-tRNA synthetaseA, B484Trypanosoma bruceiMutation(s): 0 
Gene Names: SerRSTb11.02.5020
EC: 6.1.1.11
UniProt
Find proteins for Q384V4 (Trypanosoma brucei brucei (strain 927/4 GUTat10.1))
Explore Q384V4 
Go to UniProtKB:  Q384V4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ384V4
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ATP
Query on ATP

Download Ideal Coordinates CCD File 
C [auth A],
G [auth B]
ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
 Ligand Interaction
MLI
Query on MLI

Download Ideal Coordinates CCD File 
D [auth A],
E [auth A]
MALONATE ION
C3 H2 O4
OFOBLEOULBTSOW-UHFFFAOYSA-L
 Ligand Interaction
NA
Query on NA

Download Ideal Coordinates CCD File 
F [auth A]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.195 
  • R-Value Work: 0.168 
  • R-Value Observed: 0.169 
  • Space Group: H 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 175.652α = 90
b = 175.652β = 90
c = 248.518γ = 120
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
Blu-Icedata collection
HKL-2000data reduction
HKL-2000data scaling
REFMACphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-03-02
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2017-11-01
    Changes: Refinement description