6S1M Replication date Jun 19, 2019
title Human Polymerase Delta Holoenzyme Conformer 1
authors C.Lancey, S.M.Hamdan, A.De Biasio
compound source
Molecule: Dna Polymerase Delta Catalytic Subunit
Chain: A
Synonym: Dna Polymerase Subunit Delta P125
Ec: 2.7.7.7,3.1.11.-
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Pold1, Pold
Expression_system: Spodoptera Frugiperda
Expression_system_common: Fall Armyworm
Expression_system_taxid: 7108
Expression_system_cell_line: Sf9
Expression_system_vector_type: Bacmid

Molecule: Dna Polymerase Delta Subunit 2
Chain: B
Synonym: Dna Polymerase Delta Subunit P50
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Pold2
Expression_system: Spodoptera Frugiperda
Expression_system_common: Fall Armyworm
Expression_system_taxid: 7108
Expression_system_cell_line: Sf9
Expression_system_vector_type: Bacmid

Molecule: Dna Polymerase Delta Subunit 3
Chain: C
Synonym: Dna Polymerase Delta Subunit C,Dna Polymerase Delt P66,Dna Polymerase Delta Subunit P68;
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Pold3, Kiaa0039
Expression_system: Spodoptera Frugiperda
Expression_system_common: Fall Armyworm
Expression_system_taxid: 7108
Expression_system_cell_line: Sf9
Expression_system_vector_type: Bacmid

Molecule: Dna Polymerase Delta Subunit 4
Chain: D
Synonym: Dna Polymerase Delta Subunit P12
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Pold4, Polds
Expression_system: Spodoptera Frugiperda
Expression_system_common: Fall Armyworm
Expression_system_taxid: 7108
Expression_system_cell_line: Sf9
Expression_system_vector_type: Bacmid

Molecule: Proliferating Cell Nuclear Antigen
Chain: E, F, G
Synonym: Pcna,Cyclin
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Pcna
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008

Molecule: Dna Primer
Chain: P
Engineered: Yes

Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630

Molecule: Dna Template
Chain: 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 4.27 Å
ligand DOC, SF4, TTP, ZN enzyme Transferase E.C.2.7.7.7 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A

  • nucleotide-excision repair c...
  • B


    C


    D


    F, G, E


    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (381 Kb) [Save to disk]
  • Biological Unit Coordinates (6s1m.pdb1.gz) 372 Kb
  • LPC: Ligand-Protein Contacts for 6S1M
  • CSU: Contacts of Structural Units for 6S1M
  • Retrieve 6S1M in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 6S1M from S2C, [Save to disk]
  • View 6S1M 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 6S1M
  • 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 6s1m from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [6s1m_G] [6s1m_D] [6s1m_F] [6s1m_A] [6s1m_C] [6s1m_E] [6s1m_T] [6s1m_P] [6s1m_B]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 6S1M
  • Community annotation for 6S1M at PDBWiki (http://pdbwiki.org)

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