2JD5	Transferase	date	Jan 04, 2007
title	Sky1p Bound To Npl3p-Derived Substrate Peptide
authors	B.Nolen, R.Lukasiewicz, J.A.Adams, D.Huang, G.Ghosh
compound		source
Molecule: Serinethreonine-Protein Kinase Sky1 Chain: A, B Fragment: Residues 138-306,539-742 Synonym: Sky1p, Srpk Ec: 2.7.11.1 Engineered: Yes		Organism_scientific: Saccharomyces Cerevisiae Organism_common: Baker'S Yeast Organism_taxid: 4932 Expression_system: Escherichia Coli Expression_system_taxid: 469008 Expression_system_strain: Bl21(De3) Expression_system_plasmid: Pet15b
Molecule: Nucleolar Protein 3 Chain: C Fragment: Unp Residues 408-414 Synonym: Mitochondrial Targeting Suppressor 1 Protein, Nucl Polyadenylated Rna-Binding Protein 1, Npl3p; Engineered: Yes		Synthetic: Yes Organism_scientific: Saccharomyces Cerevisiae Organism_common: Baker'S Yeast Organism_taxid: 4932
symmetry	Space Group: P 21 21 21	R_factor 0.210 R_Free 0.255
crystal cell	length a length b length c angle alpha angle beta angle gamma 72.328 88.558 134.408 90.00 90.00 90.00
method	X-Ray Diffraction	resolution	2.50 Å
ligand	MG, SO4	enzyme	Transferase E.C.2.7.11.1 BRENDA
Gene Ontology	Chain Function Process Component A, B
Primary reference	The RGG domain of Npl3p recruits Sky1p through docking interactions., Lukasiewicz R, Nolen B, Adams JA, Ghosh G, J Mol Biol. 2007 Mar 16;367(1):249-61. Epub 2006 Dec 19. PMID:17239901

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (123 Kb) [Save to disk] Biological Unit Coordinates (2jd5.pdb1.gz) 118 Kb LPC: Ligand-Protein Contacts for 2JD5 CSU: Contacts of Structural Units for 2JD5 Likely Quarternary Molecular Structure file(s) for 2JD5 Structure Factors (455 Kb) Retrieve 2JD5 in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 2JD5 from S2C, [Save to disk] Re-refined 2jd5 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 2JD5 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 2JD5

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 3D motif for 2JD5, from MSDmotif at EBI

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [2jd5_C] [2jd5] [2jd5_B] [2jd5_A] SWISS-PROT database: [Q03656] Domain organization of [SKY1_YEAST] by SWISSPFAM Domain found in 2JD5: [S_TKc ] by SMART

Other resources with information on 2JD5

Community annotation for 2JD5 at PDBWiki (http://pdbwiki.org) MMDB (Entrez's Structure Database)

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