5K1X

Catalytic domain of polyspecific pyrrolysyl-tRNA synthetase mutant Y306A/N346A/C348A/Y384F in complex with AMPPNP

  • Classification: LIGASE
  • Organism(s): Methanosarcina mazei
  • Expression System: Escherichia coli BL21(DE3)
  • Mutation(s): Yes 

  • Deposited: 2016-05-18 Released: 2016-10-19 
  • Deposition Author(s): Weber, A.
  • Funding Organization(s): National Institutes of Health/National Cancer Institute (NIH/NCI), National Science Foundation (NSF, United States), Welch Foundation, German Research Foundation (DFG)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.199 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history. 


Literature

Genetically encoded fluorophenylalanines enable insights into the recognition of lysine trimethylation by an epigenetic reader.

Lee, Y.J., Schmidt, M.J., Tharp, J.M., Weber, A., Koenig, A.L., Zheng, H., Gao, J., Waters, M.L., Summerer, D., Liu, W.R.

(2016) Chem Commun (Camb) 52: 12606-12609

  • DOI: https://doi.org/10.1039/c6cc05959g
  • Primary Citation of Related Structures:  
    5K1P, 5K1X

  • PubMed Abstract: 

    Fluorophenylalanines bearing 2-5 fluorine atoms at the phenyl ring have been genetically encoded by amber codon. Replacement of F59, a phenylalanine residue that is directly involved in interactions with trimethylated K9 of histone H3, in the Mpp8 chromodomain recombinantly with fluorophenylalanines significantly impairs the binding to a K9-trimethylated H3 peptide.

    • Organizational Affiliation: 

    Department of Chemistry, Texas A&M University, College Station, TX 7743, USA. wliu@chem.tamu.edu.


Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Pyrrolysine--tRNA ligase274Methanosarcina mazeiMutation(s): 4 
Gene Names: pylS, MM_1445
EC: 6.1.1.26
UniProt
Find proteins for Q8PWY1 (Methanosarcina mazei (strain ATCC BAA-159 / DSM 3647 / Goe1 / Go1 / JCM 11833 / OCM 88))
Explore Q8PWY1 
Go to UniProtKB:  Q8PWY1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8PWY1
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ANP
Query on ANP
Download Ideal Coordinates CCD File 
B [auth A]PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
C10 H17 N6 O12 P3
PVKSNHVPLWYQGJ-KQYNXXCUSA-N
PEG
Query on PEG
Download Ideal Coordinates CCD File 
F [auth A]DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
EDO
Query on EDO
Download Ideal Coordinates CCD File 
E [auth A]1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
CL
Query on CL
Download Ideal Coordinates CCD File 
G [auth A]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG
Query on MG
Download Ideal Coordinates CCD File 
C [auth A],
D [auth A]		MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.199 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 102.017α = 90
b = 44.14β = 100.01
c = 64.309γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
Cootmodel building

Structure Validation

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Ligand Structure Quality Assessment 


View more in-depth experimental data
Entry History & Funding Information

Deposition Data

  • Released Date: 2016-10-19 
    • Deposition Author(s): Weber, A.
Funding OrganizationLocationGrant Number
National Institutes of Health/National Cancer Institute (NIH/NCI)United StatesCA161156
National Science Foundation (NSF, United States)United StatesCHEM-1148684
Welch FoundationUnited StatesA-1715
German Research Foundation (DFG)GermanySU 726/6-1

Revision History  (Full details and data files)

  • Version 1.0: 2016-10-19
    Type: Initial release
  • Version 1.1: 2016-11-02
    Changes: Database references
  • Version 1.2: 2017-09-27
    Changes: Author supporting evidence, Derived calculations
  • Version 1.3: 2019-11-27
    Changes: Author supporting evidence
  • Version 1.4: 2024-03-06
    Changes: Data collection, Database references, Derived calculations