3ZXI

Crystal structure of human mitochondrial tyrosyl-tRNA synthetase in complex with a tyrosyl-adenylate analog


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.75 Å
  • R-Value Free: 0.307 
  • R-Value Work: 0.224 
  • R-Value Observed: 0.228 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Exploiting Protein Engineering and Crystal Polymorphism for Successful X-Ray Structure Determination

Bonnefond, L.Schellenberger, P.Basquin, J.Demangeat, G.Ritzenthaler, C.Chenevert, R.Balg, C.Frugier, M.Rudinger-Thirion, J.Giege, R.Lorber, B.Sauter, C.

(2011) Cryst Growth Des 11: 4334


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
TYROSYL-TRNA SYNTHETASE, MITOCHONDRIAL
A, B
356Homo sapiensMutation(s): 0 
EC: 6.1.1.1
UniProt & NIH Common Fund Data Resources
Find proteins for Q9Y2Z4 (Homo sapiens)
Explore Q9Y2Z4 
Go to UniProtKB:  Q9Y2Z4
PHAROS:  Q9Y2Z4
GTEx:  ENSG00000139131 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9Y2Z4
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
TYA
Query on TYA

Download Ideal Coordinates CCD File 
C [auth A],
D [auth B]
PHOSPHORIC ACID 2-AMINO-3-(4-HYDROXY-PHENYL)-PROPYL ESTER ADENOSIN-5'YL ESTER
C19 H24 N6 O8 P
JJLCVHBFTXDJMM-KFAHYOAQSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.75 Å
  • R-Value Free: 0.307 
  • R-Value Work: 0.224 
  • R-Value Observed: 0.228 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 53.14α = 90
b = 62.87β = 90
c = 196.32γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
AMoREphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-11-16
    Type: Initial release
  • Version 1.1: 2019-03-06
    Changes: Data collection, Experimental preparation, Other
  • Version 1.2: 2019-05-08
    Changes: Data collection, Experimental preparation
  • Version 1.3: 2023-12-20
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description