2BC4 Immune System date Oct 18, 2005
title Crystal Structure Of Hla-Dm
authors M.J.Nicholson, B.Moradi, N.P.Seth, X.Xing, G.D.Cuny, R.L.Stein, K.W.Wucherpfennig
compound source
Molecule: Hla Class II Histocompatibility Antigen, Dm Alpha
Chain: A, C
Synonym: Mhc Class II Antigen Dma
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Hla-Dma, Dma, Ring6
Expression_system: Drosophila Melanogaster
Expression_system_common: Fruit Fly
Expression_system_taxid: 7227
Expression_system_vector_type: Stable Transfection Plasmid
Expression_system_plasmid: Prmha-3

Molecule: Hla Class II Histocompatibility Antigen, Dm Beta
Chain: B, D
Synonym: Mhc Class II Antigen Dmb
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Hla-Dmb, Dmb, Ring7
Expression_system: Drosophila Melanogaster
Expression_system_common: Fruit Fly
Expression_system_taxid: 7227
Expression_system_vector_type: Stable Transfection Plasmid
Expression_system_plasmid: Prmha-3
symmetry Space Group: P 21 21 21
R_factor 0.229 R_Free 0.268
crystal
cell
length a length b length c angle alpha angle beta angle gamma
98.068 108.420 110.207 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.27 Å
ligand BMA, CL, NAG, NDG enzyme
Gene
Ontology
ChainFunctionProcessComponent
A, C


D, B


Primary referenceSmall molecules that enhance the catalytic efficiency of HLA-DM., Nicholson MJ, Moradi B, Seth NP, Xing X, Cuny GD, Stein RL, Wucherpfennig KW, J Immunol. 2006 Apr 1;176(7):4208-20. PMID:16547258
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (139 Kb) [Save to disk]
  • Biological Unit Coordinates (2bc4.pdb1.gz) 67 Kb
  • Biological Unit Coordinates (2bc4.pdb2.gz) 69 Kb
  • Biological Unit Coordinates (2bc4.pdb3.gz) 132 Kb
  • LPC: Ligand-Protein Contacts for 2BC4
  • CSU: Contacts of Structural Units for 2BC4
  • Likely Quarternary Molecular Structure file(s) for 2BC4
  • Structure Factors (491 Kb)
  • Retrieve 2BC4 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2BC4 from S2C, [Save to disk]
  • Re-refined 2bc4 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 2BC4 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 2BC4
  • 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 2BC4, from MSDmotif at EBI
  • Fold representative 2bc4 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2bc4_D] [2bc4_A] [2bc4_C] [2bc4] [2bc4_B]
  • SWISS-PROT database: [P28068]
  • Domain organization of [DMB_HUMAN] by SWISSPFAM
  • Domains found in 2BC4: [IGc1] [MHC_II_alpha] [MHC_II_beta ] by SMART
  • Other resources with information on 2BC4
  • Community annotation for 2BC4 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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