4LXL Oxidoreductase Peptide date Jul 30, 2013
title Crystal Structure Of Jmjd2b Complexed With Pyridine-2,4-Dica Acid And H3k9me3
authors W.C.Wang, C.H.Chu, C.C.Chen
compound source
Molecule: Lysine-Specific Demethylase 4b
Chain: A
Fragment: Catalytic Domain, Unp Residues 1-348
Synonym: Jmjc Domain-Containing Histone Demethylation Prote Jumonji Domain-Containing Protein 2b;
Ec: 1.14.11.-
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Kdm4b
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: H3 Peptide
Chain: D
Engineered: Yes

Synthetic: Yes
Organism_scientific: Human
Organism_common: Homo Sapiens
Organism_taxid: 9606
Other_details: This Sequence Occurs Naturally In Humans.
symmetry Space Group: P 21 21 21
R_factor 0.176 R_Free 0.222
length a length b length c angle alpha angle beta angle gamma
54.364 78.475 83.893 90.00 90.00 90.00
method X-Ray Diffractionresolution 1.87 Å
ligand M3L, NI, PD2, ZN enzyme Oxidoreductase E.C.1.14.11 BRENDA
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (66 Kb) [Save to disk]
  • Biological Unit Coordinates (4lxl.pdb1.gz) 61 Kb
  • LPC: Ligand-Protein Contacts for 4LXL
  • CSU: Contacts of Structural Units for 4LXL
  • Structure Factors (740 Kb)
  • Retrieve 4LXL in mmCIF format [Save to disk]
  • Re-refined 4lxl structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 4LXL 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 4LXL
  • 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 4LXL, from MSDmotif at EBI
  • Fold representative 4lxl from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4lxl_A] [4lxl_D] [4lxl]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 4LXL: [JmjC] [JmjN ] by SMART
  • Other resources with information on 4LXL
  • Community annotation for 4LXL at PDBWiki (http://pdbwiki.org)

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