1JL5	Toxin	date	Jul 15, 2001
title	Novel Molecular Architecture Of Yopm-A Leucine-Rich Effector Protein From Yersinia Pestis
authors	A.G.Evdokimov, D.E.Anderson, K.M.Routzahn, D.S.Waugh
compound		source
Molecule: Outer Protein Yopm Chain: A Engineered: Yes		Organism_scientific: Yersinia Pestis Organism_common: Bacteria Gene: Yopm Expression_system: Escherichia Coli Expression_system_common: Bacteria Expression_system_strain: Bl21de3 Expression_system_vector_type: Modified Pmal
symmetry	Space Group: I 41 2 2	R_factor	0.220
crystal cell	length a length b length c angle alpha angle beta angle gamma 149.430 149.430 191.180 90.00 90.00 90.00
method	X-Ray Diffraction	resolution	2.10 Å
ligand	CA	enzyme
note	1JL5 is a representative structure
related structures	by homologous chain: 1G9U
similarity	Contains 15 lrr (leucine-rich) repeats.[LRR_1]
subunit	Homotetramer forming a hollow cylinder with an inner diameter of approximately 35 angstroms.
subcellular loc.	Outer membrane and secreted.
Genes	Y0059, Y5054, YOP48, YOPM, YPCD1.26C (Y. pestis); YP (Y. pestis)
Gene Ontology	Chain Function Process Component A calcium ion binding protein binding metal ion binding membrane outer membrane
Primary reference	Unusual molecular architecture of the Yersinia pestis cytotoxin YopM: a leucine-rich repeat protein with the shortest repeating unit., Evdokimov AG, Anderson DE, Routzahn KM, Waugh DS, J Mol Biol 2001 Sep 28;312(4):807-21. PMID:11575934

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (69 Kb) [Save to disk] Biological Unit Coordinates (1jl5.pdb1.gz) 249 Kb CSU: Contacts of Structural Units for 1JL5 Likely Quarternary Molecular Structure file(s) for 1JL5 Structure Factors (879 Kb) Retrieve 1JL5 in mmCIF format [Save to disk]

View 1JL5 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. On AstexViewer, from MSD-EBI (viewer documentation). On RasMol (Install RasMol freeware) Here's help on how to use RasMol.

Visual 3D analysis of 1JL5

Protein Explorer, Easier to use and more powerful than RasMol. (Win and Mac only) Noncovalent Bond Finder displays the closest contacts to ligand or interface, reports distances, walks over water bridges. Cartoon representation from PDB Cartoon 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 Crystal Contacts, from CryCo at Weizmann Institute 3D motif for 1JL5, from MSDmotif at EBI Classification of representative domains in scop (Structural Classification of Proteins)     - Domain d1jl5a_, region A [Jmol] [rasmolscript] [script source] Fold representative 1jl5 from FSSP and Dali (Families of Structurally Similar Proteins) 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: [1jl5_A]

Other resources with information on 1JL5

InterPro: IPR001611 , IPR007088 PDBREPORT (protein verification by WHAT_CHECK procedures) MMDB (Entrez's Structure Database)

Movements, Movies and Images

Images from IMB Jena Image Library of Biological Macromolecules.

You may enter another PDB ID code

Go [Back], to the [PDB Lite page], to the [OCA Search page] or to the [PDB Home page]

---

OCA© by Jaime Prilusky, 1996-2007
Bioinformatics and Biological Computing
Weizmann Institute of Science

---