3L9Q Transferase date Jan 05, 2010
title Crystal Structure Of Human Polymerase Alpha-Primase P58 Iron Cluster Domain
authors S.Vaithiyalingam, B.F.Eichman, W.J.Chazin
compound source
Molecule: Dna Primase Large Subunit
Chain: A, B
Fragment: Iron-Sulfur Cluster Domain (Unp Residues 272-464)
Synonym: Dna Primase 58 Kda Subunit, P58
Ec: 2.7.7.-
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Prim2, Prim2a
Expression_system: Escherichia Coli
Expression_system_taxid: 562
symmetry Space Group: C 1 2 1
R_factor 0.130 R_Free 0.169
length a length b length c angle alpha angle beta angle gamma
109.441 53.050 88.844 90.00 115.09 90.00
method X-Ray Diffractionresolution 1.70 Å
ligand SF4, SO4 enzyme Transferase E.C.2.7.7 BRENDA
A, B

Primary referenceInsights into eukaryotic DNA priming from the structure and functional interactions of the 4Fe-4S cluster domain of human DNA primase., Vaithiyalingam S, Warren EM, Eichman BF, Chazin WJ, Proc Natl Acad Sci U S A. 2010 Aug 3;107(31):13684-9. Epub 2010 Jul 19. PMID:20643958
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (144 Kb) [Save to disk]
  • Biological Unit Coordinates (3l9q.pdb1.gz) 275 Kb
  • Biological Unit Coordinates (3l9q.pdb2.gz) 139 Kb
  • LPC: Ligand-Protein Contacts for 3L9Q
  • CSU: Contacts of Structural Units for 3L9Q
  • Structure Factors (378 Kb)
  • Retrieve 3L9Q in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3L9Q from S2C, [Save to disk]
  • Re-refined 3l9q structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
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  • Visual 3D analysis of 3L9Q
  • 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
  • 3D motif for 3L9Q, from MSDmotif at EBI
  • Fold representative 3l9q from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3l9q_A] [3l9q_B] [3l9q]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 3L9Q
  • Community annotation for 3L9Q at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
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