3QDK	Transferase	date	Jan 18, 2011
title	Structural Insight On Mechanism And Diverse Substrate Select Strategy Of Ribulokinase
authors	R.Agarwal, S.K.Burley, S.Swaminathan, New York Sgx Research Cen Structural Genomics (Nysgxrc)
compound		source
Molecule: Ribulokinase Chain: A, B, C, D Ec: 2.7.1.16 Engineered: Yes		Organism_scientific: Bacillus Halodurans Organism_taxid: 86665 Gene: Arab, Bh1872 Expression_system: Escherichia Coli Expression_system_taxid: 469008 Expression_system_strain: Bl21(De3)Ripl Expression_system_vector_type: Plasmid Expression_system_plasmid: Psgx3
symmetry	Space Group: P 1 21 1	R_factor 0.224 R_Free 0.274
crystal cell	length a length b length c angle alpha angle beta angle gamma 56.683 88.840 230.525 90.00 92.75 90.00
method	X-Ray Diffraction	resolution	2.31 Å
ligand	QDK	enzyme	Transferase E.C.2.7.1.16 BRENDA
note	3QDK supersedes 3JVP
Gene Ontology	Chain Function Process Component A, D, C, B ribulokinase activity
Primary reference	Structural insight into mechanism and diverse substrate selection strategy of L-ribulokinase., Agarwal R, Burley SK, Swaminathan S, Proteins. 2012 Jan;80(1):261-8. doi: 10.1002/prot.23202. Epub 2011 Nov 9. PMID:22072612

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (340 Kb) [Save to disk] Biological Unit Coordinates (3qdk.pdb1.gz) 167 Kb Biological Unit Coordinates (3qdk.pdb2.gz) 172 Kb LPC: Ligand-Protein Contacts for 3QDK CSU: Contacts of Structural Units for 3QDK Structure Factors (751 Kb) Retrieve 3QDK in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 3QDK from S2C, [Save to disk] Re-refined 3qdk structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 3QDK 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 3QDK

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 3QDK, from MSDmotif at EBI

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [3qdk_A] [3qdk] [3qdk_B] [3qdk_C] [3qdk_D] SWISS-PROT database: Domain organization of by SWISSPFAM

Other resources with information on 3QDK

Community annotation for 3QDK at PDBWiki (http://pdbwiki.org) MMDB (Entrez's Structure Database)

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