1RKD	Carbohydrate Kinase	date	Nov 29, 1997
title	E. Coli Ribokinase Complexed With Ribose And Adp
authors	J.A.Sigrell, A.D.Cameron, T.A.Jones, S.L.Mowbray
compound		source
Molecule: Ribokinase Chain: A Ec: 2.7.1.15 Engineered: Yes		Organism_scientific: Escherichia Coli Organism_taxid: 83333 Strain: K12 Cell_line: S2 Cellular_location: Cytoplasm Gene: Rbsk Expression_system: Escherichia Coli Expression_system_taxid: 562 Expression_system_strain: Mri240 Expression_system_plasmid: Pjgk10 Other_details: The Rbsk Gene Was Cloned Behind A Trp-Promot Forming The Plasmid Pjgk10
symmetry	Space Group: P 61 2 2	R_factor 0.220 R_Free 0.258
crystal cell	length a length b length c angle alpha angle beta angle gamma 95.400 95.400 154.870 90.00 90.00 120.00
method	X-Ray Diffraction	resolution	1.84 Å
ligand	ADP, PO4, RIB	enzyme	Transferase E.C.2.7.1.15 BRENDA
related structures	by homologous chain: 1RK2
Gene Ontology	Chain Function Process Component A
Primary reference	Structure of Escherichia coli ribokinase in complex with ribose and dinucleotide determined to 1.8 A resolution: insights into a new family of kinase structures., Sigrell JA, Cameron AD, Jones TA, Mowbray SL, Structure 1998 Feb 15;6(2):183-93. PMID:9519409

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (55 Kb) [Save to disk] Biological Unit Coordinates (1rkd.pdb1.gz) 98 Kb LPC: Ligand-Protein Contacts for 1RKD CSU: Contacts of Structural Units for 1RKD Likely Quarternary Molecular Structure file(s) for 1RKD Structure Factors (357 Kb) Retrieve 1RKD in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 1RKD from S2C, [Save to disk] Re-refined 1rkd structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 1RKD 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 1RKD

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 1RKD, from MSDmotif at EBI Genome occurence of 1RKD's fold from GeneCensus Classification of representative domains in scop (Structural Classification of Proteins)     - Domain d1rkd__, region [Jmol] [rasmolscript] [script source] Class (fold), Architecture (subfold), Topology, Homologous superfamily from CATH Summaries and structural analyses of PDB data files from PDBSum Identification of Protein Pockets & Cavities at CASTp

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [1rkd] [1rkd_A] SWISS-PROT database: [P0A9J6] Domain organization of [RBSK_ECOLI] by SWISSPFAM

Other resources with information on 1RKD

Community annotation for 1RKD at PDBWiki (http://pdbwiki.org) MMDB (Entrez's Structure Database)

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