1V7N 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, N, O
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, J, K
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, Y, Z
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
Mutation: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Escherichia Coli
Expression_system_taxid: 562
symmetry Space Group: P 1 21 1
R_factor 0.167 R_Free 0.305
crystal
cell
length a length b length c angle alpha angle beta angle gamma
133.038 46.582 191.359 90.00 90.28 90.00
method X-Ray Diffractionresolution 3.30 Å
Gene
Ontology
ChainFunctionProcessComponent
Z, X, Y, V


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] (364 Kb) [Save to disk]
  • Biological Unit Coordinates (1v7n.pdb1.gz) 94 Kb
  • Biological Unit Coordinates (1v7n.pdb2.gz) 94 Kb
  • Biological Unit Coordinates (1v7n.pdb3.gz) 93 Kb
  • Biological Unit Coordinates (1v7n.pdb4.gz) 93 Kb
  • CSU: Contacts of Structural Units for 1V7N
  • Likely Quarternary Molecular Structure file(s) for 1V7N
  • Structure Factors (535 Kb)
  • Retrieve 1V7N in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1V7N from S2C, [Save to disk]
  • Re-refined 1v7n structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 1V7N 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 1V7N
  • 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 1V7N, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1v7nh1, region H:1-116 [Jmol] [rasmolscript] [script source]
        - Domain d1v7nh2, region H:117-217 [Jmol] [rasmolscript] [script source]
        - Domain d1v7ni1, region I:1-116 [Jmol] [rasmolscript] [script source]
        - Domain d1v7ni2, region I:117-217 [Jmol] [rasmolscript] [script source]
        - Domain d1v7nj1, region J:1-116 [Jmol] [rasmolscript] [script source]
        - Domain d1v7nj2, region J:117-217 [Jmol] [rasmolscript] [script source]
        - Domain d1v7nk1, region K:1-116 [Jmol] [rasmolscript] [script source]
        - Domain d1v7nk2, region K:117-217 [Jmol] [rasmolscript] [script source]
        - Domain d1v7nl1, region L:1-107 [Jmol] [rasmolscript] [script source]
        - Domain d1v7nl2, region L:108-213 [Jmol] [rasmolscript] [script source]
        - Domain d1v7nm1, region M:1-107 [Jmol] [rasmolscript] [script source]
        - Domain d1v7nm2, region M:108-212 [Jmol] [rasmolscript] [script source]
        - Domain d1v7nn1, region N:1-107 [Jmol] [rasmolscript] [script source]
        - Domain d1v7nn2, region N:108-212 [Jmol] [rasmolscript] [script source]
        - Domain d1v7no1, region O:1-107 [Jmol] [rasmolscript] [script source]
        - Domain d1v7no2, region O:108-213 [Jmol] [rasmolscript] [script source]
        - Domain d1v7nv_, region V [Jmol] [rasmolscript] [script source]
        - Domain d1v7nx_, region X [Jmol] [rasmolscript] [script source]
        - Domain d1v7ny_, region Y [Jmol] [rasmolscript] [script source]
        - Domain d1v7nz_, region Z [Jmol] [rasmolscript] [script source]
  • Fold representative 1v7n 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: [1v7n_K] [1v7n_V] [1v7n] [1v7n_M] [1v7n_O] [1v7n_L] [1v7n_Y] [1v7n_H] [1v7n_I] [1v7n_J] [1v7n_Z] [1v7n_X] [1v7n_N]
  • SWISS-PROT database: [P40225]
  • Domain organization of [TPO_HUMAN] by SWISSPFAM
  • Domains found in 1V7N: [IG_like] [IGv ] by SMART
  • Alignments of the sequence of 1V7N with the sequences similar proteins can be viewed for 1V7N's classification [TPO_HUMAN] 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 [TPO_HUMAN] at ProtoMap. Click on the Cluster number.
  • Other resources with information on 1V7N
  • Community annotation for 1V7N 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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