1BZD Binding Protein date Oct 28, 1998
title Tertiary Structures Of Three Amyloidogenic Transthyretin Var Implications For Amyloid Fibril Formation
authors N.Schormann, J.R.Murrell, M.D.Benson
compound source
Molecule: Protein (Transthyretin)
Chain: A, B
Synonym: Prealbumin
Engineered: Yes
Mutation: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_cell_line: Hb101
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pcz11
Other_details: Variant Was Produced By Site Directed Mutage Using The Normal R-Ttr-Pcz11 Construct
symmetry Space Group: P 21 21 2
R_factor 0.188 R_Free 0.265
crystal
cell
length a length b length c angle alpha angle beta angle gamma
43.400 86.120 65.480 90.00 90.00 90.00
method X-Ray Diffractionresolution 1.90 Å
related structures by homologous chain: 1DVZ, 1TLM
Gene
Ontology
ChainFunctionProcessComponent
A, B


Primary referenceTertiary structures of amyloidogenic and non-amyloidogenic transthyretin variants: new model for amyloid fibril formation., Schormann N, Murrell JR, Benson MD, Amyloid 1998 Sep;5(3):175-87. PMID:9818054
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (45 Kb) [Save to disk]
  • Biological Unit Coordinates (1bzd.pdb1.gz) 81 Kb
  • CSU: Contacts of Structural Units for 1BZD
  • Likely Quarternary Molecular Structure file(s) for 1BZD
  • Structure Factors (110 Kb)
  • Retrieve 1BZD in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1BZD from S2C, [Save to disk]
  • Re-refined 1bzd structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 1BZD 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 1BZD
  • 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 1BZD, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1bzda_, region A [Jmol] [rasmolscript] [script source]
        - Domain d1bzdb_, region B [Jmol] [rasmolscript] [script source]
  • Fold representative 1bzd 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: [1bzd] [1bzd_A] [1bzd_B]
  • SWISS-PROT database: [P02766]
  • Domain organization of [TTHY_HUMAN] by SWISSPFAM
  • Domain found in 1BZD: [TR_THY ] by SMART
  • Alignments of the sequence of 1BZD with the sequences similar proteins can be viewed for 1BZD's classification [TTHY_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 [TTHY_HUMAN] at ProtoMap. Click on the Cluster number.
  • Other resources with information on 1BZD
  • Community annotation for 1BZD at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
  • Movements, Movies and Images
  • Domain movements in 1BZD from the Database of Macromolecular Movements.
  • Images from IMB Jena Image Library of Biological Macromolecules.

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