1BND Complex (Growth Factor Growth Factor) date Dec 12, 1994
title Structure Of The Brain-Derived Neurotrophic Factor(Slash)Neu Heterodimer
authors R.C.Robinson, C.Radziejewski, D.I.Stuart, E.Y.Jones
compound source
Molecule: Brain Derived Neurotrophic Factor
Chain: A
Synonym: Bdnf
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Organ: Brain
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Other_details: Supplied By Regeneron Pharm.

Molecule: Neurotrophin 3
Chain: B
Synonym: Nt3
Engineered: Yes
Other_details: Heterodimer

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Organ: Brain
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Other_details: Supplied By Regeneron Pharm.
symmetry Space Group: C 1 2 1
R_factor 0.182 R_Free NULL
crystal
cell
length a length b length c angle alpha angle beta angle gamma
98.400 45.100 68.000 90.00 118.30 90.00
method X-Ray Diffractionresolution 2.30 Å
ligand IPA enzyme
note 1BND is a representative structure
related structures by homologous chain: 1B8K, 1B8M, 1NT3
Primary referenceStructure of the brain-derived neurotrophic factor/neurotrophin 3 heterodimer., Robinson RC, Radziejewski C, Stuart DI, Jones EY, Biochemistry 1995 Apr 4;34(13):4139-46. PMID:7703225
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (44 Kb) [Save to disk]
  • Biological Unit Coordinates (1bnd.pdb1.gz) 79 Kb
  • Biological Unit Coordinates (1bnd.pdb2.gz) 40 Kb
  • LPC: Ligand-Protein Contacts for 1BND
  • CSU: Contacts of Structural Units for 1BND
  • Likely Quarternary Molecular Structure file(s) for 1BND
  • Retrieve 1BND in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1BND from S2C, [Save to disk]
  • View 1BND 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 1BND
  • 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 1BND, from MSDmotif at EBI
  • Genome occurence of 1BND's fold from GeneCensus
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1bnda_, region A [Jmol] [rasmolscript] [script source]
        - Domain d1bndb_, region B [Jmol] [rasmolscript] [script source]
  • Fold representative 1bnd 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: [1bnd_A] [1bnd] [1bnd_B]
  • SWISS-PROT database: [P23560] [P20783]
  • Domain organization of [BDNF_HUMAN] [NTF3_HUMAN] by SWISSPFAM
  • Domain found in 1BND: [NGF ] by SMART
  • Alignments of the sequence of 1BND with the sequences similar proteins can be viewed for 1BND's classification [BDNF_HUMAN] [NTF3_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] [NTF3_HUMAN] at ProtoMap. Click on the Cluster number.
  • Other resources with information on 1BND
  • Community annotation for 1BND 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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