3P5D Sugar Binding Protein date Oct 08, 2010
title Structure Of The Carbohydrate-Recognition Domain Of Human La With Man5 (Man Alpha1-3(Man Alpha1-6)Man Alpha1-6)(Man- Alp
authors H.Feinberg, M.E.Taylor, N.Razi, R.Mcbride, Y.A.Knirel, S.A.Graham K.Drickamer, W.I.Weis
compound source
Molecule: C-Type Lectin Domain Family 4 Member K
Chain: A, B, C, D
Fragment: Langerin Crd (Unp Residues 193-328)
Synonym: Langerin
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Cd207, Clec4k
Expression_system: Escherichia Coli
Expression_system_taxid: 83333
Expression_system_strain: Ja221
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Piniiiompa2
symmetry Space Group: P 42
R_factor 0.174 R_Free 0.220
length a length b length c angle alpha angle beta angle gamma
79.340 79.340 89.670 90.00 90.00 90.00
method X-Ray Diffractionresolution 1.80 Å
ligand CA, MAN enzyme
Primary referenceStructural Basis for Langerin Recognition of Diverse Pathogen and Mammalian Glycans through a Single Binding Site., Feinberg H, Taylor ME, Razi N, McBride R, Knirel YA, Graham SA, Drickamer K, Weis WI, J Mol Biol. 2010 Nov 26. PMID:21112338
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (102 Kb) [Save to disk]
  • Biological Unit Coordinates (3p5d.pdb1.gz) 26 Kb
  • Biological Unit Coordinates (3p5d.pdb2.gz) 26 Kb
  • Biological Unit Coordinates (3p5d.pdb3.gz) 26 Kb
  • Biological Unit Coordinates (3p5d.pdb4.gz) 26 Kb
  • LPC: Ligand-Protein Contacts for 3P5D
  • CSU: Contacts of Structural Units for 3P5D
  • Structure Factors (374 Kb)
  • Retrieve 3P5D in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3P5D from S2C, [Save to disk]
  • Re-refined 3p5d structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3P5D 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 3P5D
  • 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 3P5D, from MSDmotif at EBI
  • Fold representative 3p5d from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3p5d_D] [3p5d_B] [3p5d] [3p5d_A] [3p5d_C]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 3P5D: [CLECT ] by SMART
  • Other resources with information on 3P5D
  • Community annotation for 3P5D 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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