2E56 Lipid Binding Protein date Dec 19, 2006
title Crystal Structure Of Human Md-2
authors U.Ohto, Y.Satow
compound source
Molecule: Lymphocyte Antigen 96
Chain: A
Synonym: Md-2 Protein, Esop-1
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Ly96, Esop1, Md2
Expression_system: Pichia Pastoris
Expression_system_taxid: 4922
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Ppic9, Ppicza, Ppic6a
symmetry Space Group: P 41 21 2
R_factor 0.194 R_Free 0.249
length a length b length c angle alpha angle beta angle gamma
53.113 53.113 111.447 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.00 Å
ligand MYR, NAG enzyme
note 2E56 is a representative structure

Primary referenceCrystal structures of human MD-2 and its complex with antiendotoxic lipid IVa., Ohto U, Fukase K, Miyake K, Satow Y, Science. 2007 Jun 15;316(5831):1632-4. PMID:17569869
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (34 Kb) [Save to disk]
  • Biological Unit Coordinates (2e56.pdb1.gz) 28 Kb
  • LPC: Ligand-Protein Contacts for 2E56
  • CSU: Contacts of Structural Units for 2E56
  • Likely Quarternary Molecular Structure file(s) for 2E56
  • Structure Factors (138 Kb)
  • Retrieve 2E56 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2E56 from S2C, [Save to disk]
  • Re-refined 2e56 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 2E56 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 2E56
  • 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 2E56, from MSDmotif at EBI
  • Fold representative 2e56 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2e56_A] [2e56]
  • SWISS-PROT database: [Q9Y6Y9]
  • Domain organization of [LY96_HUMAN] by SWISSPFAM
  • Domain found in 2E56: [ML ] by SMART
  • Other resources with information on 2E56
  • Community annotation for 2E56 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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