1B8M Growth Factor Neurotrophin-4 date Feb 01, 1999
title Brain Derived Neurotrophic Factor, Neurotrophin-4
authors R.C.Robinson, C.Radziejewski, D.I.Stuart, E.Y.Jones, S.Choe
compound source
Molecule: Protein (Brain Derived Neurotrophic Factor)
Chain: A
Synonym: Bdnf
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Other_details: Supplied By Regeneron Pharm.

Molecule: Protein (Neurotrophin-4)
Chain: B
Synonym: Nt4
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Other_details: Supplied By Regeneron Pharm.
symmetry Space Group: P 21 21 2
R_factor 0.198 R_Free 0.279
crystal
cell
length a length b length c angle alpha angle beta angle gamma
50.700 105.900 51.800 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.75 Å
related structures by homologous chain: 1B98, 1BND, 1HCF
Gene
Ontology
ChainFunctionProcessComponent
A, B


Primary referenceThe structures of the neurotrophin 4 homodimer and the brain-derived neurotrophic factor/neurotrophin 4 heterodimer reveal a common Trk-binding site., Robinson RC, Radziejewski C, Spraggon G, Greenwald J, Kostura MR, Burtnick LD, Stuart DI, Choe S, Jones EY, Protein Sci 1999 Dec;8(12):2589-97. PMID:10631974
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (38 Kb) [Save to disk]
  • Biological Unit Coordinates (1b8m.pdb1.gz) 34 Kb
  • CSU: Contacts of Structural Units for 1B8M
  • Likely Quarternary Molecular Structure file(s) for 1B8M
  • Retrieve 1B8M in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1B8M from S2C, [Save to disk]
  • View 1B8M 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 1B8M
  • Cartoon representation from PDB Cartoon
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • 3D motif for 1B8M, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1b8ma_, region A [Jmol] [rasmolscript] [script source]
        - Domain d1b8mb_, region B [Jmol] [rasmolscript] [script source]
  • Fold representative 1b8m 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: [1b8m_A] [1b8m] [1b8m_B]
  • SWISS-PROT database: [P23560] [P34130]
  • Domain organization of [BDNF_HUMAN] [NTF4_HUMAN] by SWISSPFAM
  • Domain found in 1B8M: [NGF ] by SMART
  • Alignments of the sequence of 1B8M with the sequences similar proteins can be viewed for 1B8M's classification [BDNF_HUMAN] [NTF4_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 [BDNF_HUMAN] [NTF4_HUMAN] at ProtoMap. Click on the Cluster number.
  • Other resources with information on 1B8M
  • Community annotation for 1B8M 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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