6P1H Dna Binding Protein Dna date May 19, 2019
title Cryo-Em Structure Of Dna Polymerase Delta Holoenzyme
authors R.Jain, W.Rice, A.K.Aggarwal
compound source
Molecule: Dna Polymerase Delta Catalytic Subunit
Chain: A
Synonym: Dna Polymerase III
Ec: 2.7.7.7
Engineered: Yes
 Organism_scientific: Saccharomyces Cerevisiae (Strain Atcc S288c);
Organism_common: Baker'S Yeast
Organism_taxid: 559292
Strain: Atcc 204508 S288c
Variant: Atcc 204508 S288c
Gene: Pol3, Cdc2, Tex1, Ydl102w, D2366
Expression_system: Saccharomyces Cerevisiae
Expression_system_taxid: 4932

Molecule: Dna Polymerase Delta Small Subunit
Chain: B
Synonym: Hydroxyurea-Sensitive Protein 2
Ec: 2.7.7.7
Engineered: Yes
Organism_scientific: Saccharomyces Cerevisiae (Strain Atcc S288c);
Organism_common: Baker'S Yeast
Organism_taxid: 559292
Strain: Atcc 204508 S288c
Variant: Atcc 204508 S288c
Gene: Pol31, Hus2, Hys2, Sdp5, Yjr006w, J1427, Yjr83.7
Expression_system: Saccharomyces Cerevisiae
Expression_system_taxid: 4932

Molecule: Dna Polymerase Delta Subunit 3
Chain: C
Engineered: Yes
Organism_scientific: Saccharomyces Cerevisiae (Strain Atcc S288c);
Organism_common: Baker'S Yeast
Organism_taxid: 559292
Strain: Atcc 204508 S288c
Variant: Atcc 204508 S288c
Gene: Pol32, Yjr043c, J1626
Expression_system: Saccharomyces Cerevisiae
Expression_system_taxid: 4932

Molecule: Dna (30-Mer)
Chain: P, T
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 3.20 Å
ligand CA, DCP, SF4 enzyme Transferase E.C.2.7.7.7 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A
  • nuclease activity
  • exonuclease activity
  • 3'-5'-exodeoxyribonuclease a...


    • B
  • single-stranded DNA 3'-5' ex...


    • C
  • single-stranded DNA 3'-5' ex...


    • Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (239 Kb) [Save to disk]
  • Biological Unit Coordinates (6p1h.pdb1.gz) 232 Kb
  • LPC: Ligand-Protein Contacts for 6P1H
  • CSU: Contacts of Structural Units for 6P1H
  • Retrieve 6P1H in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 6P1H from S2C, [Save to disk]
    • View 6P1H 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 6P1H
  • Ramachandran plot from PDBSum
    • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [6p1h_T] [6p1h_P] [6p1h_C] [6p1h_B] [6p1h_A]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
    • Other resources with information on 6P1H
  • Community annotation for 6P1H at PDBWiki (http://pdbwiki.org)

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