2E3P Lipid Transport date Nov 28, 2006
title Crystal Structure Of Cert Start Domain In Complex With C16- Cearmide (P1)
authors N.Kudo, K.Kumagai, S.Wakatsuki, M.Nishijima, K.Hanada, R.Kato
compound source
Molecule: Lipid-Transfer Protein Cert
Chain: A, B
Fragment: Cert Start Domain (Residues 347-598)
Synonym: Goodpasture-Antigen Binding Protein, Gpbp, Cdna Flj34532 Fis, Clone Hlung2008235, Highly Similar To Homo Sapiens Goodpasture Antigen-Binding Protein (Col4a3bp)Mrna;
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Cert
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Dh5alpha
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pgex-5x1 (Modified)
symmetry Space Group: P 1
R_factor 0.217 R_Free 0.251
crystal
cell
length a length b length c angle alpha angle beta angle gamma
45.976 49.699 62.365 77.72 71.06 82.10
method X-Ray Diffractionresolution 1.40 Å
ligand 16C enzyme
Gene
Ontology
ChainFunctionProcessComponent
A, B


Primary referenceStructural basis for specific lipid recognition by CERT responsible for nonvesicular trafficking of ceramide., Kudo N, Kumagai K, Tomishige N, Yamaji T, Wakatsuki S, Nishijima M, Hanada K, Kato R, Proc Natl Acad Sci U S A. 2008 Jan 15;105(2):488-93. Epub 2008 Jan 9. PMID:18184806
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (92 Kb) [Save to disk]
  • Biological Unit Coordinates (2e3p.pdb1.gz) 46 Kb
  • Biological Unit Coordinates (2e3p.pdb2.gz) 44 Kb
  • LPC: Ligand-Protein Contacts for 2E3P
  • CSU: Contacts of Structural Units for 2E3P
  • Likely Quarternary Molecular Structure file(s) for 2E3P
  • Structure Factors (654 Kb)
  • Retrieve 2E3P in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2E3P from S2C, [Save to disk]
  • Re-refined 2e3p structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 2E3P 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 2E3P
  • 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 2E3P, from MSDmotif at EBI
  • Fold representative 2e3p from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2e3p_B] [2e3p_A] [2e3p]
  • SWISS-PROT database: [Q9Y5P4]
  • Domain organization of [C43BP_HUMAN] by SWISSPFAM
  • Domain found in 2E3P: [START ] by SMART
  • Other resources with information on 2E3P
  • Community annotation for 2E3P 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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