1K9I Sugar Binding Protein date Oct 29, 2001
title Complex Of Dc-Sign And Glcnac2man3
authors H.Feinberg, D.A.Mitchell, K.Drickamer, W.I.Weis
compound source
Molecule: Mdc-Sign1b Type I Isoform
Chain: A, B, C, D, E, F, G, H, I, J
Fragment: Carbohydrate Recognition Domain
Synonym: Dc-Sign Receptor (Dendritic Cell-Specific Icam-3 G Nonintegrin);
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Escherichia Coli
Expression_system_taxid: 562
symmetry Space Group: C 1 2 1
R_factor 0.213 R_Free 0.258
crystal
cell
length a length b length c angle alpha angle beta angle gamma
106.805 148.161 112.991 90.00 91.03 90.00
method X-Ray Diffractionresolution 2.50 Å
ligand CA, MAN, NAG enzyme
related structures by homologous chain: 1XAR
Primary referenceStructural basis for selective recognition of oligosaccharides by DC-SIGN and DC-SIGNR., Feinberg H, Mitchell DA, Drickamer K, Weis WI, Science 2001 Dec 7;294(5549):2163-6. PMID:11739956
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (240 Kb) [Save to disk]
  • Biological Unit Coordinates (1k9i.pdb1.gz) 225 Kb
  • LPC: Ligand-Protein Contacts for 1K9I
  • CSU: Contacts of Structural Units for 1K9I
  • Likely Quarternary Molecular Structure file(s) for 1K9I
  • Structure Factors (498 Kb)
  • Retrieve 1K9I in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1K9I from S2C, [Save to disk]
  • Re-refined 1k9i structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 1K9I 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 1K9I
  • 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 1K9I, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1k9ia_, region A [Jmol] [rasmolscript] [script source]
        - Domain d1k9ib_, region B [Jmol] [rasmolscript] [script source]
        - Domain d1k9ic_, region C [Jmol] [rasmolscript] [script source]
        - Domain d1k9id_, region D [Jmol] [rasmolscript] [script source]
        - Domain d1k9ie_, region E [Jmol] [rasmolscript] [script source]
        - Domain d1k9if_, region F [Jmol] [rasmolscript] [script source]
        - Domain d1k9ig_, region G [Jmol] [rasmolscript] [script source]
        - Domain d1k9ih_, region H [Jmol] [rasmolscript] [script source]
        - Domain d1k9ii_, region I [Jmol] [rasmolscript] [script source]
        - Domain d1k9ij_, region J [Jmol] [rasmolscript] [script source]
  • Fold representative 1k9i from FSSP and Dali (Families of Structurally Similar Proteins)
  • Class (fold), Architecture (subfold), Topology, Homologous superfamily from CATH
  • Summaries and structural analyses of PDB data files from PDBSum
  • Identification of Protein Pockets & Cavities at CASTp
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [1k9i_A] [1k9i] [1k9i_E] [1k9i_G] [1k9i_D] [1k9i_B] [1k9i_J] [1k9i_F] [1k9i_I] [1k9i_C] [1k9i_H]
  • SWISS-PROT database: [Q9NNX6]
  • Domain organization of [CD209_HUMAN] by SWISSPFAM
  • Domain found in 1K9I: [CLECT ] by SMART
  • Other resources with information on 1K9I
  • Community annotation for 1K9I 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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