3V6O Immune System date Dec 20, 2011
title Leptin Receptor-Antibody Complex
authors B.Carpenter, G.R.Hemsworth, R.J.Ross, P.J.Artymiuk
compound source
Molecule: Leptin Receptor
Chain: A, B
Fragment: Leptin Binding Domain Of Human Obesity Receptor
Synonym: Lep-R, Hub219, Ob Receptor, Ob-R
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Db, Lepr, Obr
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21(De3)-Ripl
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet21a(+)

Molecule: Monoclonal Antibody 9f8 Fab Fragment Heavy Chain
Chain: C, D
Fragment: Fab Fragment Of Monoclonal Antibody H Chain

Organism_scientific: Mus Musculus
Organism_taxid: 10090

Molecule: Monoclonal Antibody 9f8 Fab Fragment Light Chain
Chain: E, F
Fragment: Fab Fragment Of Monoclonal Antibody L Chain

Organism_scientific: Mus Musculus
Organism_taxid: 10090
symmetry Space Group: P 21 21 21
R_factor 0.171 R_Free 0.214
crystal
cell
length a length b length c angle alpha angle beta angle gamma
89.814 118.829 171.281 90.00 90.00 90.00
method X-Ray Diffractionresolution 1.95 Å
ligand ACT, CYS, EDO, NA, NAG enzyme
note 3V6O (Molecule of the Month:pdb149)
Gene
Ontology
ChainFunctionProcessComponent
A, B


Primary referenceStructure of the human obesity receptor leptin-binding domain reveals the mechanism of leptin antagonism by a monoclonal antibody., Carpenter B, Hemsworth GR, Wu Z, Maamra M, Strasburger CJ, Ross RJ, Artymiuk PJ, Structure. 2012 Mar 7;20(3):487-97. PMID:22405007
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (430 Kb) [Save to disk]
  • Biological Unit Coordinates (3v6o.pdb1.gz) 214 Kb
  • Biological Unit Coordinates (3v6o.pdb2.gz) 212 Kb
  • LPC: Ligand-Protein Contacts for 3V6O
  • CSU: Contacts of Structural Units for 3V6O
  • Structure Factors (1964 Kb)
  • Retrieve 3V6O in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3V6O from S2C, [Save to disk]
  • Re-refined 3v6o structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3V6O 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 3V6O
  • 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 3V6O, from MSDmotif at EBI
  • Fold representative 3v6o from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3v6o_D] [3v6o_E] [3v6o_F] [3v6o] [3v6o_A] [3v6o_C] [3v6o_B]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 3V6O: [IG_like] [IGv ] by SMART
  • Other resources with information on 3V6O
  • Community annotation for 3V6O at PDBWiki (http://pdbwiki.org)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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