5YTF Transferase Dna date Nov 17, 2017
title Structure Of Large Fragment Of Dna Polymerase I From Thermus Host-Guest Complex With The Unnatural Base M-Fc Pair With D
authors H.Zeng, M.Mondal, R.Y.Song, J.Zhang, B.Xia, Y.Q.Gao, C.Q.Yi
compound source
Molecule: Dna Polymerase I, Thermostable
Chain: A
Fragment: Large Fragment
Synonym: Taq Polymerase 1
Ec: 2.7.7.7
Engineered: Yes
Organism_scientific: Thermus Aquaticus
Organism_taxid: 271
Gene: Pola, Pol1
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Dna (5'-D(Gpapcpcpapcpgpgpcpgpcp(Doc)
Chain: B
Engineered: Yes

Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630

Molecule: Dna (5'-D(Apapapcpgpgpcpgpcpcpgp(92f) Pgpgptpc)-3');
Chain: C
Engineered: Yes

Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630
symmetry Space Group: P 31 2 1
R_factor 0.181 R_Free 0.233
crystal
cell
length a length b length c angle alpha angle beta angle gamma
107.690 107.690 90.319 90.00 90.00 120.00
method X-Ray Diffractionresolution 1.98 Å
ligand 92F, DGT, DOC, GOL, MG enzyme Transferase E.C.2.7.7.7 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceUnnatural Cytosine Bases Recognized as Thymines by DNA Polymerases by the Formation of the Watson-Crick Geometry., Zeng H, Mondal M, Song R, Zhang J, Xia B, Liu M, Zhu C, He B, Gao YQ, Yi C, Angew Chem Int Ed Engl. 2019 Jan 2;58(1):130-133. doi: 10.1002/anie.201807845., Epub 2018 Dec 5. PMID:30407705
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (218 Kb) [Save to disk]
  • Biological Unit Coordinates (5ytf.pdb1.gz) 211 Kb
  • LPC: Ligand-Protein Contacts for 5YTF
  • CSU: Contacts of Structural Units for 5YTF
  • Structure Factors (1781 Kb)
  • Retrieve 5YTF in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5YTF from S2C, [Save to disk]
  • View 5YTF in 3D
  • Proteopedia, because life has more than 2D.
  • On Jmol, a nice Rasmol like molecule viewer. This is good for easiest viewing of basic structure.
  • On FirstGlance, an excellent tool for a guided tour on the structure components, by E. Martz.
  • Visual 3D analysis of 5YTF
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5ytf_A] [5ytf_C] [5ytf_B]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 5YTF
  • Community annotation for 5YTF at PDBWiki (http://pdbwiki.org)

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