6AQG

Crystal Structure of Lysyl-tRNA Synthetase from Mycobacterium ulcerans complexed with L-lysine and Cladosporin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.195 
  • R-Value Work: 0.153 
  • R-Value Observed: 0.154 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Crystal Structure of Lysyl-tRNA Synthetase from Mycobacterium ulcerans complexed with L-lysine and Cladosporin

Dranow, D.M.Lorimer, D.D.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, C, D
506Mycobacterium ulcerans Agy99Mutation(s): 0 
Gene Names: lysSMUL_4181
EC: 6.1.1.6
UniProt
Find proteins for A0PV47 (Mycobacterium ulcerans (strain Agy99))
Explore A0PV47 
Go to UniProtKB:  A0PV47
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0PV47
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
KRS
Query on KRS

Download Ideal Coordinates CCD File 
F [auth A],
K [auth B],
Q [auth C],
U [auth D]
cladosporin
C16 H20 O5
WOMKDMUZNBFXKG-ZWKOPEQDSA-N
LYS
Query on LYS

Download Ideal Coordinates CCD File 
E [auth A],
J [auth B],
P [auth C],
T [auth D]
LYSINE
C6 H15 N2 O2
KDXKERNSBIXSRK-YFKPBYRVSA-O
MPD
Query on MPD

Download Ideal Coordinates CCD File 
G [auth A]
H [auth A]
I [auth A]
L [auth B]
M [auth B]
G [auth A],
H [auth A],
I [auth A],
L [auth B],
M [auth B],
N [auth B],
O [auth B],
R [auth C],
S [auth D]
(4S)-2-METHYL-2,4-PENTANEDIOL
C6 H14 O2
SVTBMSDMJJWYQN-YFKPBYRVSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.195 
  • R-Value Work: 0.153 
  • R-Value Observed: 0.154 
  • Space Group: P 1
  • Diffraction Data: https://doi.org/10.18430/M36AQG
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 94.12α = 90.05
b = 97.2β = 104.28
c = 105.83γ = 117.86
Software Package:
Software NamePurpose
XSCALEdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACTdata extraction
XDSdata reduction

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2017-08-30
    Type: Initial release
  • Version 1.1: 2023-10-04
    Changes: Data collection, Database references, Refinement description