2EKQ	Oxidoreductase	date	Mar 23, 2007
title	Structure Of Tt0495 Protein From Thermus Thermophilus
authors	N.K.Lokanath, K.J.Pampa, Riken Structural Genomicsproteomics Initiative (Rsgi)
compound		source
Molecule: 2-Deoxy-D-Gluconate 3-Dehydrogenase Chain: A, B, C, D Synonym: Gluconate Dehydrogenase Ec: 1.1.1.125 Engineered: Yes		Organism_scientific: Thermus Thermophilus Organism_taxid: 300852 Strain: Hb8 Expression_system: Escherichia Coli Bl21(De3) Expression_system_taxid: 469008 Expression_system_strain: Bl21(De3) Expression_system_vector_type: Plasmid Expression_system_plasmid: Pet-11a
symmetry	Space Group: P 41 21 2	R_factor 0.180 R_Free 0.208
crystal cell	length a length b length c angle alpha angle beta angle gamma 110.531 110.531 200.851 90.00 90.00 90.00
method	X-Ray Diffraction	resolution	1.80 Å
ligand	GOL, SO4	enzyme	Oxidoreductase E.C.1.1.1.125 BRENDA
Gene Ontology	Chain Function Process Component A, D, C, B
Primary reference	The first crystal structure of NAD-dependent 3-dehydro-2-deoxy-D-gluconate dehydrogenase from Thermus thermophilus HB8., Pampa KJ, Lokanath NK, Kunishima N, Rai RV, Acta Crystallogr D Biol Crystallogr. 2014 Apr 1;70(Pt 4):994-1004. doi:, 10.1107/S1399004713034925. Epub 2014 Mar 19. PMID:24699644

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (169 Kb) [Save to disk] Biological Unit Coordinates (2ekq.pdb1.gz) 164 Kb Biological Unit Coordinates (2ekq.pdb2.gz) 85 Kb Biological Unit Coordinates (2ekq.pdb3.gz) 82 Kb Biological Unit Coordinates (2ekq.pdb4.gz) 85 Kb Biological Unit Coordinates (2ekq.pdb5.gz) 82 Kb LPC: Ligand-Protein Contacts for 2EKQ CSU: Contacts of Structural Units for 2EKQ Likely Quarternary Molecular Structure file(s) for 2EKQ Structure Factors (944 Kb) Retrieve 2EKQ in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 2EKQ from S2C, [Save to disk] Re-refined 2ekq structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 2EKQ 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 2EKQ

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 2EKQ, from MSDmotif at EBI

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [2ekq_A] [2ekq_B] [2ekq_C] [2ekq_D] [2ekq] SWISS-PROT database: [Q53W82] Domain organization of [Q53W82_THET8] by SWISSPFAM

Other resources with information on 2EKQ

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

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