6H8P Oxidoreductase date Aug 03, 2018
title Jmjd2a Kdm4a Complexed With Ni(II), Nog And Histone H1.4(18 Peptide (15-Mer)
authors R.Chowdhury, L.J.Walport, C.J.Schofield
compound source
Molecule: Lysine-Specific Demethylase 4a
Chain: A, B
Synonym: Jmjc Domain-Containing Histone Demethylation Prote Jumonji Domain-Containing Protein 2a;
Ec: 1.14.11.-
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Kdm4a, Jhdm3a, Jmjd2, Jmjd2a, Kiaa0677
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008
Expression_system_variant: R3
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pnic28-Bsa4

Molecule: Histone H1.4
Chain: C, D
Synonym: Histone H1b,Histone H1s-4
Engineered: Yes

Synthetic: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
symmetry Space Group: P 21 21 2
R_factor 0.192 R_Free 0.212
crystal
cell
length a length b length c angle alpha angle beta angle gamma
100.722 150.146 57.601 90.00 90.00 90.00
method X-Ray Diffractionresolution 1.98 Å
ligand
enzyme Oxidoreductase E.C.1.14.11 BRENDA
Primary referenceMechanistic and Structural Studies of KDM-Catalysed Demethylation of Histone 1 Isotype 4 at Lysine 26., Walport LJ, Hopkinson RJ, Chowdhury R, Zhang Y, Bonnici J, Schiller R, Kawamura A, Schofield CJ, FEBS Lett. 2018 Aug 29. doi: 10.1002/1873-3468.13231. PMID:30156264
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (371 Kb) [Save to disk]
  • Biological Unit Coordinates (6h8p.pdb1.gz) 182 Kb
  • Biological Unit Coordinates (6h8p.pdb2.gz) 182 Kb
  • CSU: Contacts of Structural Units for 6H8P
  • Structure Factors (701 Kb)
  • Retrieve 6H8P in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 6H8P from S2C, [Save to disk]
  • View 6H8P 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 6H8P
  • 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
  • Fold representative 6h8p from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [6h8p_D] [6h8p_A] [6h8p_C] [6h8p_B]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 6H8P
  • Community annotation for 6H8P at PDBWiki (http://pdbwiki.org)

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