3P8M Protein Binding date Oct 14, 2010
title Human Dynein Light Chain (Dynll2) In Complex With An In Vitr Peptide Dimerized By Leucine Zipper
authors P.Rapali, L.Radnai, D.Suveges, C.Hetenyi, V.Harmat, F.Tolgyesi, W.Y.Wahlgren, G.Katona, L.Nyitray, G.Pal
compound source
Molecule: Dynein Light Chain 2
Chain: A, B
Synonym: 8 Kda Dynein Light Chain B, Dlc8b, Dynein Light Ch Type 2;
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Dynll2, Dlc2
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21(De3)Star
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet-15b

Molecule: General Control Protein Gcn4
Chain: D, C
Synonym: Amino Acid Biosynthesis Regulatory Protein
Engineered: Yes

Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Brewer'S Yeast,Lager Beer Yeast,Yeast
Organism_taxid: 4932
Gene: Gcn4, Aas3, Arg9, Yel009c
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21(De3)Star
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Modified Pet
symmetry Space Group: P 21 21 21
R_factor 0.248 R_Free 0.295
crystal
cell
length a length b length c angle alpha angle beta angle gamma
53.839 68.415 101.677 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.90 Å
Gene
Ontology
ChainFunctionProcessComponent
A, B


Primary referenceDirected evolution reveals the binding motif preference of the LC8/DYNLL hub protein and predicts large numbers of novel binders in the human proteome., Rapali P, Radnai L, Suveges D, Harmat V, Tolgyesi F, Wahlgren WY, Katona G, Nyitray L, Pal G, PLoS One. 2011 Apr 18;6(4):e18818. PMID:21533121
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (93 Kb) [Save to disk]
  • Biological Unit Coordinates (3p8m.pdb1.gz) 87 Kb
  • CSU: Contacts of Structural Units for 3P8M
  • Structure Factors (129 Kb)
  • Retrieve 3P8M in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3P8M from S2C, [Save to disk]
  • Re-refined 3p8m structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3P8M 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 3P8M
  • 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 3P8M, from MSDmotif at EBI
  • Fold representative 3p8m from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3p8m_D] [3p8m] [3p8m_C] [3p8m_B] [3p8m_A]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 3P8M: [Dynein_light ] by SMART
  • Other resources with information on 3P8M
  • Community annotation for 3P8M at PDBWiki (http://pdbwiki.org)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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