1V7M Immune System Cytokine date Dec 18, 2003
title Human Thrombopoietin Functional Domain Complexed To Neutralizing Antibody Tn1 Fab
authors M.D.Feese, T.Tamada, Y.Kato, Y.Maeda, M.Hirose, Y.Matsukura, H.Shigematsu, T.Kato, H.Miyazaki, R.Kuroki
compound source
Molecule: Monoclonal Tn1 Fab Light Chain
Chain: L, M
Fragment: Fab Light Chain
Engineered: Yes
Organism_scientific: Mus Musculus
Organism_common: House Mouse
Organism_taxid: 10090
Expression_system: Mus Musculus
Expression_system_common: House Mouse
Expression_system_taxid: 10090
Expression_system_cell_line: Hybridoma

Molecule: Monoclonal Tn1 Fab Heavy Chain
Chain: H, I
Fragment: Fab Heavy Chain
Engineered: Yes

Organism_scientific: Mus Musculus
Organism_common: House Mouse
Organism_taxid: 10090
Expression_system: Mus Musculus
Expression_system_common: House Mouse
Expression_system_taxid: 10090
Expression_system_cell_line: Hybridoma

Molecule: Thrombopoietin
Chain: V, X
Fragment: Tpo Functional Domain
Synonym: Megakaryocyte Colony Stimulating Factor, Myeloproliferative Leukemia Virus Oncogene Ligand, C-Mpl Ligand, Ml, Megakaryocyte Growth And Development Factor, Mgdf;
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Escherichia Coli
Expression_system_taxid: 562
symmetry Space Group: C 1 2 1
R_factor 0.228 R_Free 0.316
crystal
cell
length a length b length c angle alpha angle beta angle gamma
132.099 46.771 185.151 90.00 90.48 90.00
method X-Ray Diffractionresolution 2.51 Å
note 1V7M is a representative structure
related structures by homologous chain: 1JHK, 1N8Z, 1OTS, 1YEH
Primary referenceStructure of the receptor-binding domain of human thrombopoietin determined by complexation with a neutralizing antibody fragment., Feese MD, Tamada T, Kato Y, Maeda Y, Hirose M, Matsukura Y, Shigematsu H, Muto T, Matsumoto A, Watarai H, Ogami K, Tahara T, Kato T, Miyazaki H, Kuroki R, Proc Natl Acad Sci U S A 2004 Feb 17;101(7):1816-21. Epub 2004 Feb 9. PMID:14769915
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (187 Kb) [Save to disk]
  • Biological Unit Coordinates (1v7m.pdb1.gz) 92 Kb
  • Biological Unit Coordinates (1v7m.pdb2.gz) 93 Kb
  • CSU: Contacts of Structural Units for 1V7M
  • Likely Quarternary Molecular Structure file(s) for 1V7M
  • Structure Factors (521 Kb)
  • Retrieve 1V7M in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1V7M from S2C, [Save to disk]
  • Re-refined 1v7m structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 1V7M 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 1V7M
  • 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 1V7M, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1v7mh1, region H:1-116 [Jmol] [rasmolscript] [script source]
        - Domain d1v7mh2, region H:117-217 [Jmol] [rasmolscript] [script source]
        - Domain d1v7mi1, region I:1-116 [Jmol] [rasmolscript] [script source]
        - Domain d1v7mi2, region I:117-217 [Jmol] [rasmolscript] [script source]
        - Domain d1v7ml1, region L:1-107 [Jmol] [rasmolscript] [script source]
        - Domain d1v7ml2, region L:108-212 [Jmol] [rasmolscript] [script source]
        - Domain d1v7mm1, region M:1-107 [Jmol] [rasmolscript] [script source]
        - Domain d1v7mm2, region M:108-212 [Jmol] [rasmolscript] [script source]
        - Domain d1v7mv_, region V [Jmol] [rasmolscript] [script source]
        - Domain d1v7mx_, region X [Jmol] [rasmolscript] [script source]
  • Fold representative 1v7m 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: [1v7m] [1v7m_I] [1v7m_L] [1v7m_H] [1v7m_X] [1v7m_M] [1v7m_V]
  • SWISS-PROT database: [P40225]
  • Domain organization of [TPO_HUMAN] by SWISSPFAM
  • Domains found in 1V7M: [IGc1] [IGv ] by SMART
  • Other resources with information on 1V7M
  • Community annotation for 1V7M 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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