3URF Cytokine date Nov 22, 2011
title Human Ranklopg Complex
authors X.Q.Wang, X.D.Luan, Q.Y.Lu
compound source
Molecule: Tumor Necrosis Factor Ligand Superfamily Member 1 Form;
Chain: A
Fragment: Unp Residues 162-317
Synonym: Osteoclast Differentiation Factor, Odf, Osteoprote Ligand, Opgl, Receptor Activator Of Nuclear Factor Kappa-B 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: 562
Expression_system_vector_type: Plasmid

Molecule: Tumor Necrosis Factor Receptor Superfamily Member
Chain: Z
Fragment: Unp Residues 22-186
Synonym: Osteoclastogenesis Inhibitory Factor, Osteoprotege
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Tnfrsf11b, Ocif, Opg
Expression_system: Spodoptera Frugiperda
Expression_system_taxid: 7108
Expression_system_vector_type: Baculovirus
symmetry Space Group: P 41 3 2
R_factor 0.202 R_Free 0.251
crystal
cell
length a length b length c angle alpha angle beta angle gamma
144.800 144.800 144.800 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.70 Å
ligand NAG enzyme
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceCrystal Structure of Human RANKL Complexed with Its Decoy Receptor Osteoprotegerin., Luan X, Lu Q, Jiang Y, Zhang S, Wang Q, Yuan H, Zhao W, Wang J, Wang X, J Immunol. 2012 Jul 1;189(1):245-52. Epub 2012 Jun 4. PMID:22664871
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (117 Kb) [Save to disk]
  • Biological Unit Coordinates (3urf.pdb1.gz) 329 Kb
  • LPC: Ligand-Protein Contacts for 3URF
  • CSU: Contacts of Structural Units for 3URF
  • Structure Factors (114 Kb)
  • Retrieve 3URF in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3URF from S2C, [Save to disk]
  • Re-refined 3urf structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3URF 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 3URF
  • Cartoon representation from PDB Cartoon
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • 3D motif for 3URF, from MSDmotif at EBI
  • Fold representative 3urf from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3urf] [3urf_A] [3urf_Z]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 3URF: [TNF] [TNFR ] by SMART
  • Other resources with information on 3URF
  • Community annotation for 3URF at PDBWiki (http://pdbwiki.org)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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