5VC1 Cell Adhesion date Mar 30, 2017
title Crystal Structure Of L-Selectin Lectinegf Domains
authors S.Wedepohl, J.Dernedde, A.Vahedi-Faridi, R.Tauber, W.Saenger, H.B
compound source
Molecule: L-Selectin
Chain: A
Fragment: Unp Residues 39-195
Synonym: Cd62 Antigen-Like Family Member L,Leukocyte Adhesi Molecule 1,Lam-1,Leukocyte Surface Antigen Leu-8,Leukocyte- Endothelial Cell Adhesion Molecule 1,Lecam1,Lymph Node Homi Receptor,Tq1,Gp90-Mel;
Engineered: Yes
Mutation: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Sell, Lnhr, Lyam1
Expression_system: Homo Sapiens
Expression_system_common: Human
Expression_system_taxid: 9606
Expression_system_cell_line: Hek293f
symmetry Space Group: I 2 3
R_factor 0.202 R_Free 0.231
length a length b length c angle alpha angle beta angle gamma
118.598 118.598 118.598 90.00 90.00 90.00
method X-Ray Diffractionresolution 1.94 Å
ligand BMA, CA, GOL, MAN, NAG, PEG, PG4 enzyme
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (35 Kb) [Save to disk]
  • Biological Unit Coordinates (5vc1.pdb1.gz) 29 Kb
  • LPC: Ligand-Protein Contacts for 5VC1
  • CSU: Contacts of Structural Units for 5VC1
  • Structure Factors (171 Kb)
  • Retrieve 5VC1 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5VC1 from S2C, [Save to disk]
  • Re-refined 5vc1 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 5VC1 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 5VC1
  • 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
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1q5vc1, region C:1-48 [Jmol] [rasmolscript] [script source]
        - Domain d1e5vc1, region C:626-781 [Jmol] [rasmolscript] [script source]
        - Domain d1r5vc1, region C:82-182 [Jmol] [rasmolscript] [script source]
  • Fold representative 5vc1 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5vc1_A]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 5VC1
  • Community annotation for 5VC1 at PDBWiki (http://pdbwiki.org)

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