3CC5 Immune System date Feb 24, 2008
title H-2db Complex With Human Gp100
authors D.Badia-Martinez, A.Achour
compound source
Molecule: H-2 Class I Histocompatibility Antigen, D-B Alpha
Chain: A, D
Fragment: Extracellular Part, Unp Residues 25-300
Synonym: H-2db
Engineered: Yes
Organism_scientific: Mus Musculus
Organism_common: Mouse
Organism_taxid: 10090
Gene: H2-D1
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_vector_type: Plasmid

Molecule: Beta-2-Microglobulin
Chain: B, E
Engineered: Yes

Organism_scientific: Mus Musculus
Organism_common: Mouse
Organism_taxid: 10090
Gene: B2m
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_vector_type: Plasmid

Molecule: Nonameric Peptide From Melanocyte Protein Pmel 17
Chain: C, F
Fragment: Extracellular Part, Unp Residues 25-33
Synonym: Silver Locus Protein Homolog, Melanocyte Lineage-S Antigen Gp100, Melanoma-Associated Me20 Antigen, Me20m, Me2
Engineered: Yes

Synthetic: Yes
Other_details: Chemical Synthesis
symmetry Space Group: C 2 2 21
R_factor 0.228 R_Free 0.268
crystal
cell
length a length b length c angle alpha angle beta angle gamma
67.200 165.400 161.300 90.00 90.00 90.00
method X-Ray Diffractionresolution 1.91 Å
ligand GOL, SO4 enzyme
Gene
Ontology
ChainFunctionProcessComponent
E, B


Primary referenceDesign of agonistic altered peptides for the robust induction of CTL directed towards H-2Db in complex with the melanoma-associated epitope gp100., van Stipdonk MJ, Badia-Martinez D, Sluijter M, Offringa R, van Hall T, Achour A, Cancer Res. 2009 Oct 1;69(19):7784-92. Epub 2009 Sep 29. PMID:19789338
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (147 Kb) [Save to disk]
  • Biological Unit Coordinates (3cc5.pdb1.gz) 73 Kb
  • Biological Unit Coordinates (3cc5.pdb2.gz) 73 Kb
  • LPC: Ligand-Protein Contacts for 3CC5
  • CSU: Contacts of Structural Units for 3CC5
  • Likely Quarternary Molecular Structure file(s) for 3CC5
  • Structure Factors (1077 Kb)
  • Retrieve 3CC5 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3CC5 from S2C, [Save to disk]
  • Re-refined 3cc5 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3CC5 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 3CC5
  • 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 3CC5, from MSDmotif at EBI
  • Fold representative 3cc5 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3cc5_A] [3cc5] [3cc5_D] [3cc5_E] [3cc5_F] [3cc5_C] [3cc5_B]
  • SWISS-PROT database: [P01887] [P01899] [P40967]
  • Domain organization of [B2MG_MOUSE] [HA11_MOUSE] [PME17_HUMAN] by SWISSPFAM
  • Domain found in 3CC5: [IGc1 ] by SMART
  • Other resources with information on 3CC5
  • Community annotation for 3CC5 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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