1PVH Signaling Protein Cytokine date Jun 27, 2003
title Crystal Structure Of Leukemia Inhibitory Factor In Complex With Gp130
authors M.J.Boulanger, A.J.Bankovich, T.Kortemme, D.Baker, K.C.Garcia
compound source
Molecule: Interleukin-6 Receptor Beta Chain
Chain: A, C
Fragment: Domains D2 And D3
Synonym: Il-6r-Beta, Interleukin 6 Signal Transducer, Membrane Glycoprotein 130, Gp130, Oncostatin M Receptor, Cdw130, Cd130 Antigen;
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Il6st
Expression_system: Spodoptera Frugiperda
Expression_system_common: Fall Armyworm
Expression_system_taxid: 7108

Molecule: Leukemia Inhibitory Factor
Chain: B, D
Synonym: Lif, Differentiation-Stimulating Factor, D Factor, Melanoma-Derived Lpl Inhibitor, Mlpli;
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Lif Or Hilda
Expression_system: Spodoptera Frugiperda
Expression_system_common: Fall Armyworm
Expression_system_taxid: 7108
symmetry Space Group: P 21 21 21
R_factor 0.248 R_Free 0.289
crystal
cell
length a length b length c angle alpha angle beta angle gamma
79.710 86.700 146.430 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.50 Å
ligand IOD enzyme
related structures by homologous chain: 1A7M, 1BJ8, 1I1R, 1LKI
Gene
Ontology
ChainFunctionProcessComponent
D, B
  • growth factor activity


  • Primary referenceConvergent mechanisms for recognition of divergent cytokines by the shared signaling receptor gp130., Boulanger MJ, Bankovich AJ, Kortemme T, Baker D, Garcia KC, Mol Cell 2003 Sep;12(3):577-89. PMID:14527405
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (127 Kb) [Save to disk]
  • Biological Unit Coordinates (1pvh.pdb1.gz) 63 Kb
  • Biological Unit Coordinates (1pvh.pdb2.gz) 62 Kb
  • LPC: Ligand-Protein Contacts for 1PVH
  • CSU: Contacts of Structural Units for 1PVH
  • Likely Quarternary Molecular Structure file(s) for 1PVH
  • Structure Factors (275 Kb)
  • Retrieve 1PVH in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1PVH from S2C, [Save to disk]
  • Re-refined 1pvh structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 1PVH 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 1PVH
  • 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 1PVH, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1pvha1, region A:101-196 [Jmol] [rasmolscript] [script source]
        - Domain d1pvha2, region A:197-301 [Jmol] [rasmolscript] [script source]
        - Domain d1pvhb_, region B [Jmol] [rasmolscript] [script source]
        - Domain d1pvhc1, region C:101-196 [Jmol] [rasmolscript] [script source]
        - Domain d1pvhc2, region C:197-301 [Jmol] [rasmolscript] [script source]
        - Domain d1pvhd_, region D [Jmol] [rasmolscript] [script source]
  • Fold representative 1pvh 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: [1pvh_B] [1pvh_D] [1pvh_C] [1pvh] [1pvh_A]
  • SWISS-PROT database: [P40189] [P15018]
  • Domain organization of [IL6RB_HUMAN] [LIF_HUMAN] by SWISSPFAM
  • Domains found in 1PVH: [FN3] [LIF_OSM ] by SMART
  • Other resources with information on 1PVH
  • Community annotation for 1PVH at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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