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
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
  • 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 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
  • Alignments of the sequence of 3URF with the sequences similar proteins can be viewed for 3URF's classification at ProtoMap. Click on "Neighbors List", then on the "See Alignments" button below the list.
  • A sequence distance tree ("phylogenetic tree") can be viewed for 1ACL's classification at ProtoMap. Click on the Cluster number.
  • 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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