5XMA Transferase Dna date May 13, 2017
title Crystal Structure Of Asfvpolx In Complex With Dna Enzyme At Space Group
authors H.H.Liu, J.H.Gan
compound source
Molecule: Repair Dna Polymerase X
Chain: A, B
Synonym: Pol X
Ec: 2.7.7.7
Engineered: Yes
Organism_scientific: African Swine Fever Virus (Strain Bada Vero-Adapted);
Organism_common: Ba71v
Organism_taxid: 10498
Strain: Badajoz 1971 Vero-Adapted
Gene: Ba71v-97, O174l
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Dna (36-Mer)
Chain: E
Engineered: Yes

Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630

Molecule: Dnarna (5'-D(Apcpgpapgpapgpapgpapt)-R D(Pgpgptpgpcpgptptpapcpa)-3');
Chain: F
Engineered: Yes

Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630
symmetry Space Group: P 43 21 2
R_factor 0.258 R_Free 0.285
crystal
cell
length a length b length c angle alpha angle beta angle gamma
78.846 78.846 241.677 90.00 90.00 90.00
method X-Ray Diffractionresolution 3.80 Å
ligand
enzyme Transferase E.C.2.7.7.7 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A, B
  • DNA-directed DNA polymerase ...


  • Primary referenceCrystal structure of an RNA-cleaving DNAzyme., Liu H, Yu X, Chen Y, Zhang J, Wu B, Zheng L, Haruehanroengra P, Wang R, Li S, Lin J, Li J, Sheng J, Huang Z, Ma J, Gan J, Nat Commun. 2017 Dec 8;8(1):2006. doi: 10.1038/s41467-017-02203-x. PMID:29222499
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (85 Kb) [Save to disk]
  • Biological Unit Coordinates (5xma.pdb1.gz) 81 Kb
  • CSU: Contacts of Structural Units for 5XMA
  • Structure Factors (159 Kb)
  • Retrieve 5XMA in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5XMA from S2C, [Save to disk]
  • View 5XMA 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 5XMA
  • Cartoon representation from PDB Cartoon
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • Fold representative 5xma from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5xma_E] [5xma_B] [5xma_A] [5xma_F]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 5XMA
  • Community annotation for 5XMA at PDBWiki (http://pdbwiki.org)

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