1R8G	Ligase	date	Oct 24, 2003
title	Structure And Function Of Ybdk
authors	C.Lehmann, V.Doseeva, S.Pullalarevu, W.Krajewski, A.Howard, O.Her Structure 2 Function Project (S2f)
compound		source
Molecule: Hypothetical Protein Ybdk Chain: A, B Ec: 6.3.-.- Engineered: Yes		Organism_scientific: Escherichia Coli Organism_taxid: 562 Gene: Ybdk, B0581 Expression_system: Escherichia Coli Expression_system_taxid: 562 Expression_system_strain: Bl21star(De3) Expression_system_vector_type: Plasmid Expression_system_plasmid: Pet100-D-Topo
symmetry	Space Group: P 1 21 1	R_factor 0.189 R_Free 0.252
crystal cell	length a length b length c angle alpha angle beta angle gamma 49.470 100.320 71.370 90.00 99.94 90.00
method	X-Ray Diffraction	resolution	2.15 Å
ligand	MSE	enzyme	Ligase E.C.6.3 BRENDA
note	1R8G is a representative structure
related structures	by homologous chain: 1TT4
Gene Ontology	Chain Function Process Component A, B
Primary reference	YbdK is a carboxylate-amine ligase with a gamma-glutamyl:Cysteine ligase activity: crystal structure and enzymatic assays., Lehmann C, Doseeva V, Pullalarevu S, Krajewski W, Howard A, Herzberg O, Proteins 2004 Aug 1;56(2):376-83. PMID:15211520

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (131 Kb) [Save to disk] Biological Unit Coordinates (1r8g.pdb1.gz) 123 Kb LPC: Ligand-Protein Contacts for 1R8G CSU: Contacts of Structural Units for 1R8G Likely Quarternary Molecular Structure file(s) for 1R8G Structure Factors (888 Kb) Retrieve 1R8G in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 1R8G from S2C, [Save to disk] Re-refined 1r8g structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 1R8G 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 1R8G

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 1R8G, from MSDmotif at EBI Classification of representative domains in scop (Structural Classification of Proteins)     - Domain d1r8ga_, region A [Jmol] [rasmolscript] [script source]     - Domain d1r8gb_, region B [Jmol] [rasmolscript] [script source]

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [1r8g_A] [1r8g_B] [1r8g] SWISS-PROT database: [P77213] Domain organization of [CAAL_ECOLI] by SWISSPFAM

Other resources with information on 1R8G

Community annotation for 1R8G at PDBWiki (http://pdbwiki.org) MMDB (Entrez's Structure Database)

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