6KI3 Dna Binding Protein Dna date Jul 17, 2019
title The Crystal Structure Of Asfvap:Df Commplex
authors Y.Chen, J.Gan
compound source
Molecule: Probable Ap Endonuclease
Chain: A, B
Synonym: Ape
Ec: 3.1.21.-
Engineered: Yes
Organism_scientific: African Swine Fever Virus (Isolate Tic Africapretoriuskop Pr41996);
Organism_common: Asfv
Organism_taxid: 561443
Strain: Isolate Ticksouth Africapretoriuskop Pr41996
Gene: Pret-146
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008

Molecule: Dna (5'-D(Gpcpapgpcpgptpcpc)-3')
Chain: C, F
Engineered: Yes

Synthetic: Yes
Organism_scientific: African Swine Fever Virus
Organism_taxid: 10497

Molecule: Dna (5'-D(P(3dr)Pcpgpapcpgpapg)-3')
Chain: D, G
Engineered: Yes

Synthetic: Yes
Organism_scientific: African Swine Fever Virus
Organism_taxid: 10497

Molecule: Dna (5'- D(Cpcptpcpgptpcpgpgpgpgpapcpgpcptpg)-3');
Chain: E, H
Engineered: Yes

Synthetic: Yes
Organism_scientific: African Swine Fever Virus
Organism_taxid: 10497
symmetry Space Group: P 1 21 1
R_factor 0.208 R_Free 0.244
crystal
cell
length a length b length c angle alpha angle beta angle gamma
50.637 84.698 98.585 90.00 93.66 90.00
method X-Ray Diffractionresolution 2.35 Å
ligand 3DR, ZN enzyme Hydrolase E.C.3.1.21 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A, B
  • nuclease activity
  • endonuclease activity
  • exonuclease activity


  • Primary referenceA unique DNA-binding mode of African swine fever virus AP endonuclease., Chen Y, Chen X, Huang Q, Shao Z, Gao Y, Li Y, Yang C, Liu H, Li J, Wang Q, Ma J, Zhang YZ, Gu Y, Gan J, Cell Discov. 2020 Mar 17;6:13. doi: 10.1038/s41421-020-0146-2. eCollection 2020. PMID:32194979
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (128 Kb) [Save to disk]
  • Biological Unit Coordinates (6ki3.pdb1.gz) 62 Kb
  • Biological Unit Coordinates (6ki3.pdb2.gz) 63 Kb
  • LPC: Ligand-Protein Contacts for 6KI3
  • CSU: Contacts of Structural Units for 6KI3
  • Structure Factors (845 Kb)
  • Retrieve 6KI3 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 6KI3 from S2C, [Save to disk]
  • View 6KI3 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 6KI3
  • 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 6ki3 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [6ki3_B] [6ki3_H] [6ki3_C] [6ki3_E] [6ki3_D] [6ki3_G] [6ki3_F] [6ki3_A]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 6KI3
  • Community annotation for 6KI3 at PDBWiki (http://pdbwiki.org)

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