5L2X Transferase Dna date Aug 02, 2016
title Crystal Structure Of Human Primpol Ternary Complex
authors O.Rechkoblit, Y.K.Gupta, R.Malik, K.R.Rajashankar, R.E.Johnson, L S.Prakash, A.K.Aggarwal
compound source
Molecule: Dna-Directed Primasepolymerase Protein
Chain: A, B
Synonym: Hprimpol1,Coiled-Coil Domain-Containing Protein 11
Ec: 2.7.7.-
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Primpol, Ccdc111
Expression_system: Saccharomyces Cerevisiae
Expression_system_taxid: 4932

Molecule: Dna (5'-D(Ptpcpgpcp(5iu)Papcpc)-3')
Chain: C, G
Engineered: Yes

Synthetic: Yes
Organism_scientific: Homo Sapiens
Organism_taxid: 9606

Molecule: Dna (5'-D(Pgpgptpapgpcp(Ddg))-3')
Chain: D, H
Engineered: Yes

Synthetic: Yes
Organism_scientific: Homo Sapiens
Organism_taxid: 9606
symmetry Space Group: P 1
R_factor 0.206 R_Free 0.255
length a length b length c angle alpha angle beta angle gamma
50.723 65.212 72.463 67.89 85.22 86.65
method X-Ray Diffractionresolution 2.20 Å
ligand 5IU, CA, DDG, DTP enzyme Transferase E.C.2.7.7 BRENDA
A, B

Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (111 Kb) [Save to disk]
  • Biological Unit Coordinates (5l2x.pdb1.gz) 55 Kb
  • Biological Unit Coordinates (5l2x.pdb2.gz) 51 Kb
  • LPC: Ligand-Protein Contacts for 5L2X
  • CSU: Contacts of Structural Units for 5L2X
  • Structure Factors (2807 Kb)
  • Retrieve 5L2X in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5L2X from S2C, [Save to disk]
  • Re-refined 5l2x structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 5L2X 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 5L2X
  • Cartoon representation from PDB Cartoon
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Electron Density related parameters from EDS Electron Density Server, at Upsala
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • Fold representative 5l2x from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5l2x_G] [5l2x_D] [5l2x_C] [5l2x_A] [5l2x_H] [5l2x] [5l2x_B]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 5L2X
  • Community annotation for 5L2X at PDBWiki (http://pdbwiki.org)

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