2X6M Immune System date Feb 18, 2010
title Structure Of A Single Domain Camelid Antibody Fragment In Complex With A C-Terminal Peptide Of Alpha-Synuclein
authors E.Degenst, T.Guilliams, J.Wellens, E.M.O'Day, C.A.Waudby, S.Meeha M.Dumoulin, S.T.D.Hsu, N.Cremades, K.H.G.Verschueren, E.Pardon J.Steyaert, J.Christodoulou, C.M.Dobson
compound source
Molecule: Heavy Chain Variable Domain From Dromedary
Chain: A
Engineered: Yes
Other_details: Engineered From Immunised Dromedary
Organism_scientific: Camelus Dromedarius
Organism_common: Dromedary
Organism_taxid: 9838
Tissue: Blood
Cell: Lymphocyte
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Wk6
Expression_system_vector: Phen6

Molecule: Alpha-Synuclein Peptide
Chain: B
Fragment: C-Terminal Fragment Of Alpha-Synuclein, Residues

Synthetic: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
symmetry Space Group: C 2 2 21
R_factor 0.15634 R_Free 0.20258
crystal
cell
length a length b length c angle alpha angle beta angle gamma
60.170 63.120 62.870 90.00 90.00 90.00
method X-Ray Diffractionresolution 1.62 Å
Primary referenceStructure and properties of a complex of alpha-synuclein and a single-domain camelid antibody., De Genst EJ, Guilliams T, Wellens J, O'Day EM, Waudby CA, Meehan S, Dumoulin M, Hsu ST, Cremades N, Verschueren KH, Pardon E, Wyns L, Steyaert J, Christodoulou J, Dobson CM, J Mol Biol. 2010 Sep 17;402(2):326-43. Epub 2010 Jul 8. PMID:20620148
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (30 Kb) [Save to disk]
  • Biological Unit Coordinates (2x6m.pdb1.gz) 26 Kb
  • CSU: Contacts of Structural Units for 2X6M
  • Structure Factors (187 Kb)
  • Retrieve 2X6M in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2X6M from S2C, [Save to disk]
  • Re-refined 2x6m structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 2X6M 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 2X6M
  • 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 2X6M, from MSDmotif at EBI
  • Fold representative 2x6m from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2x6m_A] [2x6m_B] [2x6m]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Alignments of the sequence of 2X6M with the sequences similar proteins can be viewed for 2X6M's classification 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 at ProtoMap. Click on the Cluster number.
  • Other resources with information on 2X6M
  • Community annotation for 2X6M at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
  • Movements, Movies and Images
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