4QWC Transferase Dna date Jul 16, 2014
title Ternary Crystal Structures Of A Y-Family Dna Polymerase Dpo4 Sulfolobus Solfataricus In Complex With Dna And L-Dcdp
authors R.Vyas, Z.Suo
compound source
Molecule: Dna Polymerase Iv
Chain: A, D
Fragment: Dpo4
Synonym: Pol Iv
Ec: 2.7.7.7
Engineered: Yes
Organism_scientific: Sulfolobus Solfataricus
Organism_taxid: 273057
Strain: Atcc 35092 Dsm 1617 Jcm 11322 P2
Gene: Dbh, Dpo4, Sso2448
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_plasmid: Pet21b

Molecule: Dna (5'-D(Gpgpcptpapcpapgpgpapcptpc)
Chain: B, E
Fragment: Dna
Engineered: Yes

Synthetic: Yes
Other_details: Polydeoxyribonucleotide

Molecule: Dna (5'- D(Tptpcpapgpgpapgptpcpcptpgptpapgpcpc)-3'
Chain: C, F
Fragment: Dna
Engineered: Yes

Synthetic: Yes
Other_details: Polydeoxyribonucleotide
symmetry Space Group: P 21 21 21
R_factor 0.227 R_Free 0.277
crystal
cell
length a length b length c angle alpha angle beta angle gamma
98.440 101.930 105.400 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.40 Å
ligand ACT, CA, DOC, LTP enzyme Transferase E.C.2.7.7.7 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A, D


Primary referenceStructural and kinetic insights into binding and incorporation of L-nucleotide analogs by a Y-family DNA polymerase., Gaur V, Vyas R, Fowler JD, Efthimiopoulos G, Feng JY, Suo Z, Nucleic Acids Res. 2014 Aug 7. pii: gku709. PMID:25104018
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (298 Kb) [Save to disk]
  • Biological Unit Coordinates (4qwc.pdb1.gz) 147 Kb
  • Biological Unit Coordinates (4qwc.pdb2.gz) 147 Kb
  • LPC: Ligand-Protein Contacts for 4QWC
  • CSU: Contacts of Structural Units for 4QWC
  • Structure Factors (1688 Kb)
  • Retrieve 4QWC in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4QWC from S2C, [Save to disk]
  • Re-refined 4qwc structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 4QWC 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 4QWC
  • 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 4QWC, from MSDmotif at EBI
  • Fold representative 4qwc from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4qwc_A] [4qwc_E] [4qwc] [4qwc_F] [4qwc_C] [4qwc_B] [4qwc_D]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 4QWC
  • Community annotation for 4QWC at PDBWiki (http://pdbwiki.org)

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