5F3C	Oxidoreductase	date	Dec 02, 2015
title	Crystal Structure Of Human Kdm4a In Complex With Compound 52
authors	Y.V.Le Bihan, I.M.Westwood, R.L.M.Van Montfort
compound		source
Molecule: Lysine-Specific Demethylase 4a Chain: A, B, C, D Fragment: Unp Residues 1-359 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: Rosetta 2 Expression_system_vector_type: Plasmid Expression_system_plasmid: Pnic28
symmetry	Space Group: P 1 21 1	R_factor 0.161 R_Free 0.196
crystal cell	length a length b length c angle alpha angle beta angle gamma 58.101 101.725 142.758 90.00 99.53 90.00
method	X-Ray Diffraction	resolution	2.06 Å
ligand	5U8, CL, DMS, GOL, ZN	enzyme	Oxidoreductase E.C.1.14.11 BRENDA
Primary reference	8-Substituted Pyrido[3,4-d]pyrimidin-4(3H)-one Derivatives As Potent, Cell Permeable, KDM4 (JMJD2) and KDM5 (JARID1) Histone Lysine Demethylase Inhibitors., Bavetsias V, Lanigan RM, Ruda GF, Atrash B, McLaughlin MG, Tumber A, Mok NY, Le Bihan YV, Dempster S, Boxall KJ, Jeganathan F, Hatch SB, Savitsky P, Velupillai S, Krojer T, England KS, Sejberg J, Thai C, Donovan A, Pal A, Scozzafava G, Bennett JM, Kawamura A, Johansson C, Szykowska A, Gileadi C, Burgess-Brown NA, von Delft F, Oppermann U, Walters Z, Shipley J, Raynaud FI, Westaway SM, Prinjha RK, Fedorov O, Burke R, Schofield CJ, Westwood IM, Bountra C, Muller S, van Montfort RL, Brennan PE, Blagg J, J Med Chem. 2016 Jan 7. PMID:26741168

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (499 Kb) [Save to disk] Biological Unit Coordinates (5f3c.pdb1.gz) 126 Kb Biological Unit Coordinates (5f3c.pdb2.gz) 123 Kb Biological Unit Coordinates (5f3c.pdb3.gz) 125 Kb Biological Unit Coordinates (5f3c.pdb4.gz) 126 Kb LPC: Ligand-Protein Contacts for 5F3C CSU: Contacts of Structural Units for 5F3C Structure Factors (2847 Kb) Retrieve 5F3C in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 5F3C from S2C, [Save to disk] Re-refined 5f3c structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 5F3C 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 5F3C

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

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [5f3c_D] [5f3c_A] [5f3c_C] [5f3c_B] [5f3c] SWISS-PROT database: Domain organization of by SWISSPFAM Domains found in 5F3C: [JmjC] [JmjN ] by SMART

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