2YVK	Isomerase	date	Apr 13, 2007
title	Crystal Structure Of 5-Methylthioribose 1-Phosphate Isomeras Complex From Bacillus Subtilis
authors	H.Tamura, T.Inoue, Y.Kai, H.Matsumura
compound		source
Molecule: Methylthioribose-1-Phosphate Isomerase Chain: A, B, C, D Synonym: Mtr-1-P Isomerase, S-Methyl-5-Thioribose-1-Phospha Isomerase; Ec: 5.3.1.23 Engineered: Yes		Organism_scientific: Bacillus Subtilis Organism_taxid: 1423 Gene: Mtna Expression_system: Escherichia Coli Bl21(De3) Expression_system_taxid: 469008 Expression_system_strain: Bl21(De3) Expression_system_vector_type: Plasmid Expression_system_plasmid: Pet-15b
symmetry	Space Group: P 1 21 1	R_factor 0.212 R_Free 0.257
crystal cell	length a length b length c angle alpha angle beta angle gamma 79.987 84.444 95.299 90.00 92.34 90.00
method	X-Ray Diffraction	resolution	2.40 Å
ligand	MRU	enzyme	Isomerase E.C.5.3.1.23 BRENDA
Gene Ontology	Chain Function Process Component A, D, C, B
Primary reference	Crystal structure of 5-methylthioribose 1-phosphate isomerase product complex from Bacillus subtilis: Implications for catalytic mechanism., Tamura H, Saito Y, Ashida H, Inoue T, Kai Y, Yokota A, Matsumura H, Protein Sci. 2008 Jan;17(1):126-35. PMID:18156470

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (223 Kb) [Save to disk] Biological Unit Coordinates (2yvk.pdb1.gz) 110 Kb Biological Unit Coordinates (2yvk.pdb2.gz) 111 Kb LPC: Ligand-Protein Contacts for 2YVK CSU: Contacts of Structural Units for 2YVK Likely Quarternary Molecular Structure file(s) for 2YVK Structure Factors (327 Kb) Retrieve 2YVK in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 2YVK from S2C, [Save to disk] Re-refined 2yvk structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 2YVK 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 2YVK

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 2YVK, from MSDmotif at EBI

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [2yvk_C] [2yvk_B] [2yvk] [2yvk_D] [2yvk_A] SWISS-PROT database: [O31662] Domain organization of [MTNA_BACSU] by SWISSPFAM

Other resources with information on 2YVK

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

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