3VU8

Metionyl-tRNA synthetase from Thermus thermophilus complexed with methionyl-adenylate analogue


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.300 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.205 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.0 of the entry. See complete history


Literature

The modeling of structures of specific conformation of homosysteine-AMP leading to thiolactone-formation on class Ia aminoacyl-tRNA synthetases

Konno, M.Kato-Murayama, M.Takeda, R.Takasaka, R.Uchikawa, E.Toma-Fukai, S.Ishii, R.Nureki, O.Yokoyama, S.

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Methionine--tRNA ligaseA502Thermus thermophilus HB8Mutation(s): 0 
Gene Names: metSmetGTTHA1298
EC: 6.1.1.10
UniProt
Find proteins for P23395 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
Explore P23395 
Go to UniProtKB:  P23395
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP23395
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MDS
Query on MDS

Download Ideal Coordinates CCD File 
C [auth A]N-[METHIONYL]-N'-[ADENOSYL]-DIAMINOSULFONE
C15 H24 N8 O6 S2
DAUQVCLMADDCHF-QWRDWHBNSA-N
 Ligand Interaction
ZN
Query on ZN

Download Ideal Coordinates CCD File 
B [auth A]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.300 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.205 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 50.823α = 90
b = 82.682β = 90
c = 120.165γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
X-PLORmodel building
X-PLORrefinement
SCALEPACKdata scaling
X-PLORphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-06-26
    Type: Initial release