5BNQ	Cytokine	date	May 26, 2015
title	Crystal Structure Of Hrankl-Mrank Complex
authors	J.Ren
compound		source
Molecule: Tumor Necrosis Factor Ligand Superfamily Member 1 Chain: A Synonym: Osteoclast Differentiation Factor,Odf,Osteoprotege Ligand,Opgl,Receptor Activator Of Nuclear Factor Kappa-B Li Rankl,Tnf-Related Activation-Induced Cytokine,Trance; Engineered: Yes		Organism_scientific: Homo Sapiens Organism_common: Human Organism_taxid: 9606 Gene: Tnfsf11, Opgl, Rankl, Trance Expression_system: Escherichia Coli Expression_system_taxid: 469008 Expression_system_strain: Bl21(De3) Expression_system_variant: Gold Expression_system_vector_type: Pet28a Expression_system_plasmid: Plasmid
Molecule: Tumor Necrosis Factor Receptor Superfamily Member Chain: R Synonym: Osteoclast Differentiation Factor Receptor,Odfr,Re Activator Of Nf-Kb, Rank; Engineered: Yes		Organism_scientific: Mus Musculus Organism_common: House Mouse Organism_taxid: 10090 Gene: Tnfrsf11a, Rank Expression_system: Escherichia Coli Expression_system_taxid: 469008 Expression_system_strain: Bl21(De3) Expression_system_variant: Gold Expression_system_vector_type: Pet28a Expression_system_plasmid: Plasmid
symmetry	Space Group: P 63	R_factor 0.171 R_Free 0.203
crystal cell	length a length b length c angle alpha angle beta angle gamma 122.188 122.188 94.473 90.00 90.00 120.00
method	X-Ray Diffraction	resolution	2.80 Å
ligand	CL, NA, PO4	enzyme
Gene Ontology	Chain Function Process Component A
Primary reference	A RANKL mutant used as an inter-species vaccine for efficient immunotherapy of osteoporosis., Liu C, Zhao Y, He W, Wang W, Chen Y, Zhang S, Ma Y, Gohda J, Ishida T, Walter TS, Owens RJ, Stuart DI, Ren J, Gao B, Sci Rep. 2015 Sep 28;5:14150. doi: 10.1038/srep14150. PMID:26412210

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (113 Kb) [Save to disk] Biological Unit Coordinates (5bnq.pdb1.gz) 314 Kb LPC: Ligand-Protein Contacts for 5BNQ CSU: Contacts of Structural Units for 5BNQ Structure Factors (200 Kb) Retrieve 5BNQ in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 5BNQ from S2C, [Save to disk] Re-refined 5bnq structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 5BNQ 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 5BNQ

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

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [5bnq_R] [5bnq] [5bnq_A] SWISS-PROT database: Domain organization of by SWISSPFAM Domains found in 5BNQ: [TNF] [TNFR ] by SMART

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