5D6Y	Oxidoreductase	date	Aug 13, 2015
title	Crystal Structure Of Double Tudor Domain Of Human Lysine Dem Kdm4a Complexed With Histone H3k23me3
authors	F.Wang, Z.Su, M.D.Miller, J.M.Denu, G.N.Phillips Jr., Enzyme Disc Natural Product Biosynthesis (Natpro)
compound		source
Molecule: Lysine-Specific Demethylase 4a Chain: A, B, C, D, E, F 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 Expression_system_taxid: 469008 Expression_system_strain: Bl21(De3)
Molecule: Peptide H3k23me3 (19-28) Chain: a, b, c, d Engineered: Yes		Synthetic: Yes Organism_scientific: Homo Sapiens Organism_taxid: 9606
symmetry	Space Group: P 32	R_factor 0.264 R_Free 0.295
crystal cell	length a length b length c angle alpha angle beta angle gamma 106.159 106.159 79.206 90.00 90.00 120.00
method	X-Ray Diffraction	resolution	2.29 Å
ligand	M3L	enzyme	Oxidoreductase E.C.1.14.11 BRENDA
Primary reference	Reader domain specificity and lysine demethylase-4 family function., Su Z, Wang F, Lee JH, Stephens KE, Papazyan R, Voronina E, Krautkramer KA, Raman A, Thorpe JJ, Boersma MD, Kuznetsov VI, Miller MD, Taverna SD, Phillips GN Jr, Denu JM, Nat Commun. 2016 Nov 14;7:13387. doi: 10.1038/ncomms13387. PMID:27841353

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (244 Kb) [Save to disk] Biological Unit Coordinates (5d6y.pdb1.gz) 42 Kb Biological Unit Coordinates (5d6y.pdb2.gz) 42 Kb Biological Unit Coordinates (5d6y.pdb3.gz) 40 Kb Biological Unit Coordinates (5d6y.pdb4.gz) 40 Kb Biological Unit Coordinates (5d6y.pdb5.gz) 39 Kb Biological Unit Coordinates (5d6y.pdb6.gz) 39 Kb LPC: Ligand-Protein Contacts for 5D6Y CSU: Contacts of Structural Units for 5D6Y Structure Factors (505 Kb) Retrieve 5D6Y in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 5D6Y from S2C, [Save to disk] Re-refined 5d6y structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 5D6Y in 3D

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Visual 3D analysis of 5D6Y

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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: [5d6y_C] [5d6y_F] [5d6y_a] [5d6y_d] [5d6y_D] [5d6y_E] [5d6y] [5d6y_c] [5d6y_B] [5d6y_A] [5d6y_b] SWISS-PROT database: Domain organization of by SWISSPFAM Domain found in 5D6Y: [TUDOR ] by SMART

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