4X0P Transferase Dna date Nov 21, 2014
title Ternary Complex Of Human Dna Polymerase Theta C-Terminal Dom Binding Ddatp Opposite A Tetrahydrofuran Ap Site Analog
authors K.E.Zahn, S.Doublie
compound source
Molecule: Dna Polymerase Theta
Chain: A, B, C, D
Fragment: Unp Residues 1792-2590
Synonym: Dna Polymerase Eta
Ec: 2.7.7.7
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Polq, Polh
Expression_system: Escherichia Coli
Expression_system_taxid: 469008
Expression_system_strain: Rosetta2(De3)Plyss
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Psumo3

Molecule: Dna (5'-D(Pcpgpgpcptpgptpcpaptptpc)-3
Chain: F, H, J, L
Engineered: Yes

Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630

Molecule: Dna (5'- D(Cpgptptpgpapaptpgpapcpapgpcpcpgpcpg)-3'
Chain: E, G, I, K
Engineered: Yes

Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630
symmetry Space Group: P 21 21 21
R_factor 0.241 R_Free 0.302
crystal
cell
length a length b length c angle alpha angle beta angle gamma
126.921 136.971 247.991 90.00 90.00 90.00
method X-Ray Diffractionresolution 3.91 Å
ligand CA, DDS, GOL enzyme Transferase E.C.2.7.7.7 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A, D, C, B


Primary referenceHuman DNA polymerase theta grasps the primer terminus to mediate DNA repair., Zahn KE, Averill AM, Aller P, Wood RD, Doublie S, Nat Struct Mol Biol. 2015 Mar 16. doi: 10.1038/nsmb.2993. PMID:25775267
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (1012 Kb) [Save to disk]
  • Biological Unit Coordinates (4x0p.pdb1.gz) 250 Kb
  • Biological Unit Coordinates (4x0p.pdb2.gz) 254 Kb
  • Biological Unit Coordinates (4x0p.pdb3.gz) 253 Kb
  • Biological Unit Coordinates (4x0p.pdb4.gz) 254 Kb
  • LPC: Ligand-Protein Contacts for 4X0P
  • CSU: Contacts of Structural Units for 4X0P
  • Structure Factors (454 Kb)
  • Retrieve 4X0P in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4X0P from S2C, [Save to disk]
  • Re-refined 4x0p structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 4X0P 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 4X0P
  • 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
  • 3D motif for 4X0P, from MSDmotif at EBI
  • Fold representative 4x0p from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4x0p_A] [4x0p_I] [4x0p_H] [4x0p] [4x0p_G] [4x0p_C] [4x0p_B] [4x0p_D] [4x0p_L] [4x0p_F] [4x0p_K] [4x0p_E] [4x0p_J]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 4X0P: [POLAc ] by SMART
  • Other resources with information on 4X0P
  • Community annotation for 4X0P at PDBWiki (http://pdbwiki.org)

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