4BPX Transferase date May 28, 2013
title Crystal Structure Of Human Primase In Complex With The Prima Binding Motif Of Dna Polymerase Alpha
authors M.L.Kilkenny, R.L.Perera, L.Pellegrini
compound source
Molecule: Dna Primase Small Subunit
Chain: A, C
Synonym: Dna Primase 49 Kda Subunit, P49
Ec: 2.7.7.-
Engineered: Yes
Mutation: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Escherichia Coli
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_variant: Rosetta2
Expression_system_vector_type: Plasmid
Expression_system_vector: Prsfduet-1

Molecule: Dna Polymerase Alpha Catalytic Subunit, Dna Prima Subunit;
Chain: B, D
Fragment: Primase-Binding Motif Residues 1445-1462, Pril Re 253;
Synonym: Dna Polymerase Alpha Catalytic Subunit P180, Dna P Kda Subunit, P58;
Ec: 2.7.7.7, 2.7.7.-
Engineered: Yes
Other_details: Pril Is Fused At The N-Terminus To The Prima Motif Of Dna Polymerase Alpha (Chain E), Via A 15-Amino Aci Of Sequence Tgstgstgstgstgs

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Escherichia Coli
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_variant: Rosetta2
Expression_system_vector_type: Plasmid
Expression_system_vector: Prsfduet-1
symmetry Space Group: P 1 21 1
R_factor 0.234 R_Free 0.267
crystal
cell
length a length b length c angle alpha angle beta angle gamma
120.680 70.701 127.160 90.00 105.83 90.00
method X-Ray Diffractionresolution 3.40 Å
ligand ZN enzyme Transferase E.C.2.7.7 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A, C


D, B


Primary referenceStructures of human primase reveal design of nucleotide elongation site and mode of Pol alpha tethering., Kilkenny ML, Longo MA, Perera RL, Pellegrini L, Proc Natl Acad Sci U S A. 2013 Sep 16. PMID:24043831
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (390 Kb) [Save to disk]
  • Biological Unit Coordinates (4bpx.pdb1.gz) 196 Kb
  • Biological Unit Coordinates (4bpx.pdb2.gz) 130 Kb
  • Biological Unit Coordinates (4bpx.pdb3.gz) 64 Kb
  • LPC: Ligand-Protein Contacts for 4BPX
  • CSU: Contacts of Structural Units for 4BPX
  • Structure Factors (355 Kb)
  • Retrieve 4BPX in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4BPX from S2C, [Save to disk]
  • Re-refined 4bpx structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 4BPX 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 4BPX
  • 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 4BPX, from MSDmotif at EBI
  • Fold representative 4bpx from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4bpx_A] [4bpx_C] [4bpx_B] [4bpx] [4bpx_D]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 4BPX
  • Community annotation for 4BPX at PDBWiki (http://pdbwiki.org)

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