5Y3R Dna Binding Protein date Jul 29, 2017
title Cryo-Em Structure Of Human Dna-Pk Holoenzyme
authors X.Yin, M.Liu, Y.Tian, J.Wang, Y.Xu
compound source
Molecule: X-Ray Repair Cross-Complementing Protein 6
Chain: A
Fragment: Unp Residues 34-534
Synonym: 5'-Deoxyribose-5-Phosphate Lyase Ku70,5'-Drp Lyase Kda Subunit Of Ku Antigen,Atp-Dependent Dna Helicase 2 Subu Dependent Dna Helicase II 70 Kda Subunit,Ctc Box-Binding Fa Kda Subunit,Ctcbf,Dna Repair Protein Xrcc6,Lupus Ku Autoant Protein P70,Ku70,Thyroid-Lupus Autoantigen,Tlaa,X-Ray Repai Complementing Defective Repair In Chinese Hamster Cells 6;
Ec: 3.6.4.-,4.2.99.-
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Xrcc6, G22p1
Expression_system: Homo Sapiens
Expression_system_taxid: 9606

Molecule: X-Ray Repair Cross-Complementing Protein 5
Chain: B
Fragment: Unp Residues 6-541
Synonym: 86 Kda Subunit Of Ku Antigen,Atp-Dependent Dna Hel Subunit 2,Atp-Dependent Dna Helicase II 80 Kda Subunit,Ctc Binding Factor 85 Kda Subunit,Ctcbf,Dna Repair Protein Xrcc Ku86,Lupus Ku Autoantigen Protein P86,Nuclear Factor Iv,Thy Autoantigen,Tlaa,X-Ray Repair Complementing Defective Repai Chinese Hamster Cells 5 (Double-Strand-Break Rejoining);
Ec: 3.6.4.-
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Xrcc5, G22p2
Expression_system: Homo Sapiens
Expression_system_taxid: 9606

Molecule: Prkdc-Helix
Chain: K
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_taxid: 9606
Expression_system: Homo Sapiens
Expression_system_taxid: 9606

Molecule: Dna (34-Mer)
Chain: D
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_taxid: 9606
Expression_system: Homo Sapiens
Expression_system_taxid: 9606

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

Organism_scientific: Homo Sapiens
Organism_taxid: 9606
Expression_system: Homo Sapiens
Expression_system_taxid: 9606

Molecule: Dna-Dependent Protein Kinase Catalytic Subunit
Chain: C
Fragment: Unp Residues 10-4128
Synonym: Dna-Pkcs,Dnpk1,P460
Ec: 2.7.11.1
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Prkdc, Hyrc, Hyrc1
Expression_system: Homo Sapiens
Expression_system_taxid: 9606
Expression_system_cell_line: Hek293f
Expression_system_organ: Kidney
symmetry Space Group: P 1
R_factor
R_Free
crystal
cell
length a length b length c angle alpha angle beta angle gamma
1.000 1.000 1.000 90.00 90.00 90.00
method Electron Microscopyresolution 6.60 Å
ligand
enzyme Hydrolase E.C.3.6.4 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A


B


C


Primary referenceCryo-EM structure of human DNA-PK holoenzyme., Yin X, Liu M, Tian Y, Wang J, Xu Y, Cell Res. 2017 Aug 25. doi: 10.1038/cr.2017.110. PMID:28840859
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (724 Kb) [Save to disk]
  • Biological Unit Coordinates (5y3r.pdb1.gz) 715 Kb
  • CSU: Contacts of Structural Units for 5Y3R
  • Retrieve 5Y3R in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5Y3R from S2C, [Save to disk]
  • View 5Y3R 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 5Y3R
  • 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 5y3r from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5y3r_E] [5y3r_K] [5y3r_D] [5y3r_A] [5y3r_B] [5y3r_C]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 5Y3R
  • Community annotation for 5Y3R at PDBWiki (http://pdbwiki.org)

  • You may enter another PDB ID code
    Go [Back], to the [PDB Lite page], to the [OCA Search page] or to the [PDB Home page]
    OCA© by Jaime Prilusky, 1996-2014
    Bioinformatics Unit
    Weizmann Institute of Science