4MD4 Immune System date Aug 22, 2013
title Immune Receptor
authors S.W.Scally, J.Rossjohn
compound source
Molecule: Hla Class II Histocompatibility Antigen, Dr Alpha
Chain: A
Fragment: Extracellular Domain, Unp Residues 26-206
Synonym: Mhc Class II Antigen Dra
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Hla-Dra, Hla-Dra1
Expression_system: Homo Sapiens
Expression_system_taxid: 9606

Molecule: Hla Class II Histocompatibility Antigen, Drb1-4 B
Chain: B
Fragment: Extracellular Domain, Unp Residues 30-219
Synonym: Mhc Class II Antigen Drb14, Dr-4, Dr4
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Hla-Drb1
Expression_system: Homo Sapiens
Expression_system_taxid: 9606

Molecule: Aggrecan Core Protein
Chain: C
Fragment: Unp Residues 89-103
Synonym: Cartilage-Specific Proteoglycan Core Protein, Cspc Chondroitin Sulfate Proteoglycan Core Protein 1, Chondroiti Proteoglycan 1, Aggrecan Core Protein 2;
Engineered: Yes

Synthetic: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Other_details: This Sequence Is From Human Aggrecan And Con Citrulline At Positions 93 And 95
symmetry Space Group: C 2 2 21
R_factor 0.165 R_Free 0.209
crystal
cell
length a length b length c angle alpha angle beta angle gamma
67.091 182.580 77.539 90.00 90.00 90.00
method X-Ray Diffractionresolution 1.95 Å
ligand CIR, EDO, NAG enzyme
Gene
Ontology
ChainFunctionProcessComponent
A


B


Primary referenceA molecular basis for the association of the HLA-DRB1 locus, citrullination, and rheumatoid arthritis., Scally SW, Petersen J, Law SC, Dudek NL, Nel HJ, Loh KL, Wijeyewickrema LC, Eckle SB, van Heemst J, Pike RN, McCluskey J, Toes RE, La Gruta NL, Purcell AW, Reid HH, Thomas R, Rossjohn J, J Exp Med. 2013 Nov 18;210(12):2569-82. doi: 10.1084/jem.20131241. Epub 2013 Nov , 4. PMID:24190431
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (151 Kb) [Save to disk]
  • Biological Unit Coordinates (4md4.pdb1.gz) 143 Kb
  • LPC: Ligand-Protein Contacts for 4MD4
  • CSU: Contacts of Structural Units for 4MD4
  • Structure Factors (2028 Kb)
  • Retrieve 4MD4 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4MD4 from S2C, [Save to disk]
  • Re-refined 4md4 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 4MD4 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 4MD4
  • Cartoon representation from PDB Cartoon
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • 3D motif for 4MD4, from MSDmotif at EBI
  • Fold representative 4md4 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4md4] [4md4_A] [4md4_C] [4md4_B]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 4MD4: [IGc1] [MHC_II_alpha] [MHC_II_beta ] by SMART
  • Other resources with information on 4MD4
  • Community annotation for 4MD4 at PDBWiki (http://pdbwiki.org)

  • You may enter another PDB ID code
    Go [Back], to the [PDB Lite page], to the [OCA Search page] or to the [PDB Home page]
    OCA© by Jaime Prilusky, 1996-2014
    Bioinformatics Unit
    Weizmann Institute of Science