6NS0

Crystal Structure of Lysyl-tRNA Synthetase from Chlamydia trachomatis complexed with L-lysine and Cladosporin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.207 
  • R-Value Work: 0.164 
  • R-Value Observed: 0.165 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Crystal Structure of Lysyl-tRNA Synthetase from Chlamydia trachomatis with complexed with L-lysine and Cladosporin

Dranow, D.M.Abendroth, J.Lorimer, D.D.Horanyi, P.S.Edwards, T.E.

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Lysine--tRNA ligase
A, B
534Chlamydia trachomatis L2b/UCH-1/proctitisMutation(s): 0 
Gene Names: lysSCTLon_0150
EC: 6.1.1.6
UniProt
Find proteins for B0BAN6 (Chlamydia trachomatis serovar L2b (strain UCH-1/proctitis))
Explore B0BAN6 
Go to UniProtKB:  B0BAN6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB0BAN6
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 7 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
KRS
Query on KRS

Download Ideal Coordinates CCD File 
D [auth A],
DA [auth B]
cladosporin
C16 H20 O5
WOMKDMUZNBFXKG-ZWKOPEQDSA-N
PG4
Query on PG4

Download Ideal Coordinates CCD File 
E [auth A],
FA [auth B]
TETRAETHYLENE GLYCOL
C8 H18 O5
UWHCKJMYHZGTIT-UHFFFAOYSA-N
LYS
Query on LYS

Download Ideal Coordinates CCD File 
C [auth A],
CA [auth B]
LYSINE
C6 H15 N2 O2
KDXKERNSBIXSRK-YFKPBYRVSA-O
PEG
Query on PEG

Download Ideal Coordinates CCD File 
X [auth A]DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
EDO
Query on EDO

Download Ideal Coordinates CCD File 
AA [auth B]
BA [auth B]
EA [auth B]
F [auth A]
G [auth A]
AA [auth B],
BA [auth B],
EA [auth B],
F [auth A],
G [auth A],
GA [auth B],
H [auth A],
HA [auth B],
I [auth A],
IA [auth B],
J [auth A],
JA [auth B],
K [auth A],
KA [auth B],
L [auth A],
LA [auth B],
M [auth A],
MA [auth B],
N [auth A],
NA [auth B],
O [auth A],
OA [auth B],
P [auth A],
PA [auth B],
Q [auth A],
QA [auth B],
R [auth A],
RA [auth B],
S [auth A],
SA [auth B],
T [auth A],
U [auth A],
V [auth A],
W [auth A]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
TA [auth B]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA
Query on NA

Download Ideal Coordinates CCD File 
Y [auth A],
Z [auth A]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

Unit Cell:
Length ( Å )Angle ( ˚ )
a = 96.58α = 90
b = 57.51β = 97
c = 139.55γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
XSCALEdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2019-02-06
    Type: Initial release
  • Version 1.1: 2019-02-20
    Changes: Data collection, Structure summary
  • Version 1.2: 2023-10-11
    Changes: Data collection, Database references, Derived calculations, Refinement description