6CST Replication, Transferase Dna date Mar 21, 2018
title Structure Of Human Dna Polymerase Kappa With Dna
authors V.Jha, H.Ling
compound source
Molecule: Dna Polymerase Kappa
Chain: A, B
Synonym: Dinb Protein,Dinp
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Polk, Dinb1
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Dna (5'-D(Paptpapcpaptpapcpc)-3')
Chain: C, P
Engineered: Yes

Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630

Molecule: Dna (5'-D(Ptpapcptpgpgptpaptpgptpapt
Chain: D, T
Engineered: Yes

Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630
symmetry Space Group: P 21 21 21
R_factor 0.198 R_Free 0.234
length a length b length c angle alpha angle beta angle gamma
67.579 124.630 165.040 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.00 Å
ligand CL, DZ4, EDO, IOD, K, MG, PEG, PGE enzyme Transferase E.C. BRENDA
A, B

Primary reference2.0 A resolution crystal structure of human polkappa reveals a new catalytic function of N-clasp in DNA replication., Jha V, Ling H, Sci Rep. 2018 Oct 11;8(1):15125. doi: 10.1038/s41598-018-33371-5. PMID:30310122
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (183 Kb) [Save to disk]
  • Biological Unit Coordinates (6cst.pdb1.gz) 174 Kb
  • LPC: Ligand-Protein Contacts for 6CST
  • CSU: Contacts of Structural Units for 6CST
  • Structure Factors (3824 Kb)
  • Retrieve 6CST in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 6CST from S2C, [Save to disk]
  • View 6CST 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 6CST
  • 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 6cst from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [6cst_B] [6cst_C] [6cst_D] [6cst_A] [6cst_P] [6cst_T]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 6CST
  • Community annotation for 6CST at PDBWiki (http://pdbwiki.org)

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