6KNC Replication Dna date Aug 05, 2019
title Pold-Pcna-Dna (Form B)
authors K.Mayanagi, K.Oki, N.Miyazaki, S.Ishino, T.Yamagami, K.Iwasaki, D. K.Morikawa, T.Shirai, Y.Ishino
compound source
Molecule: Dna Polymerase II Small Subunit
Chain: A
Synonym: Dna Polymerase D Dp1 (Dna Polymerase II Small) Sub II,Exodeoxyribonuclease Small Subunit;
Ec: 2.7.7.7,3.1.11.1
Engineered: Yes
Organism_scientific: Thermococcus Kodakarensis Kod1
Organism_taxid: 69014
Strain: Atcc Baa-918 Jcm 12380 Kod1
Gene: Polb, Tk1902
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Dna Polymerase D Dp2 (Dna Polymerase II Large) Su
Chain: B
Engineered: Yes

Organism_scientific: Thermococcus Kodakarensis
Organism_taxid: 311400
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Dna Polymerase Sliding Clamp 1
Chain: C, D, E
Synonym: Proliferating Cell Nuclear Antigen Homolog 1,Pcna
Engineered: Yes

Organism_scientific: Thermococcus Kodakarensis Kod1
Organism_taxid: 69014
Strain: Atcc Baa-918 Jcm 12380 Kod1
Gene: Pcn1, Tk0535
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Pri30dna
Chain: F
Engineered: Yes

Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630

Molecule: Temp45dna
Chain: G
Engineered: Yes

Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630
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 9.30 Å
ligand FE, ZN enzyme Transferase E.C.2.7.7.7 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
D, C, E


Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (363 Kb) [Save to disk]
  • Biological Unit Coordinates (6knc.pdb1.gz) 352 Kb
  • LPC: Ligand-Protein Contacts for 6KNC
  • CSU: Contacts of Structural Units for 6KNC
  • Retrieve 6KNC in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 6KNC from S2C, [Save to disk]
  • View 6KNC 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 6KNC
  • 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 6knc from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [6knc_D] [6knc_E] [6knc_A] [6knc_G] [6knc_F] [6knc_C] [6knc_B]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 6KNC
  • Community annotation for 6KNC at PDBWiki (http://pdbwiki.org)

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