6MDX Dna Binding Protein Dna date Sep 05, 2018
title Mechanism Of Protease Dependent Dpc Repair
authors F.Li, J.Raczynska, Z.Chen, H.Yu
compound source
Molecule: Sprt-Like Domain-Containing Protein Spartan
Chain: A
Synonym: Dna Damage Protein Targeting Vcp,Dvc1,Protein With Domain At The N Terminus,Spartan;
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Sprtn, C1orf124, Dvc1, Unq1880pro4323
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Dna (5'-D(Pcpc)-3')
Chain: D
Engineered: Yes

Synthetic: Yes
Organism_scientific: Homo Sapiens
Organism_taxid: 9606
symmetry Space Group: P 21 21 2
R_factor 0.159 R_Free 0.193
crystal
cell
length a length b length c angle alpha angle beta angle gamma
128.324 29.507 50.298 90.00 90.00 90.00
method X-Ray Diffractionresolution 1.55 Å
ligand EDO, FLC, MLZ, MSE, PGE, ZN enzyme
Primary referenceStructural Insight into DNA-Dependent Activation of Human Metalloprotease Spartan., Li F, Raczynska JE, Chen Z, Yu H, Cell Rep. 2019 Mar 19;26(12):3336-3346.e4. doi: 10.1016/j.celrep.2019.02.082. PMID:30893605
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (50 Kb) [Save to disk]
  • Biological Unit Coordinates (6mdx.pdb1.gz) 44 Kb
  • LPC: Ligand-Protein Contacts for 6MDX
  • CSU: Contacts of Structural Units for 6MDX
  • Structure Factors (218 Kb)
  • Retrieve 6MDX in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 6MDX from S2C, [Save to disk]
  • View 6MDX 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 6MDX
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [6mdx_D] [6mdx_A]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 6MDX
  • Community annotation for 6MDX at PDBWiki (http://pdbwiki.org)

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