4P5M Immune System date Mar 18, 2014
title Structural Basis Of Chronic Beryllium Disease: Bridging The Between Allergic Hypersensitivity And Autoimmunity
authors Y.Wang, S.Dai, J.Kappler
compound source
Molecule: Hla Class II Histocompatibility Antigen, Dp Alpha
Chain: A, C, E, G
Fragment: Unp Residues 32-214
Synonym: Dp(W3),Dp(W4),Hla-Sb Alpha Chain,Mhc Class II Dp3- Class II Dpa1;
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Hla-Dpa1, Hla-Dp1a, Hlasb
Expression_system: Trichoplusia Ni
Expression_system_taxid: 7111

Molecule: Peptide,Hla Class II Histocompatibility Antigen, Chain;
Chain: B, D, F, H
Synonym: Hla Class II Histocompatibility Antigen,Dp(W2) Bet Mhc Class II Antigen Dpb1;
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Hla-Dpb1
Expression_system: Trichoplusia Ni
Expression_system_taxid: 7111
symmetry Space Group: P 1 21 1
R_factor 0.168 R_Free 0.204
length a length b length c angle alpha angle beta angle gamma
81.631 130.468 107.994 90.00 107.16 90.00
method X-Ray Diffractionresolution 1.70 Å
ligand BMA, NA, NAG enzyme
A, E, C, G

F, B, H, D

Primary referenceStructural basis of chronic beryllium disease: linking allergic hypersensitivity and autoimmunity., Clayton GM, Wang Y, Crawford F, Novikov A, Wimberly BT, Kieft JS, Falta MT, Bowerman NA, Marrack P, Fontenot AP, Dai S, Kappler JW, Cell. 2014 Jul 3;158(1):132-42. doi: 10.1016/j.cell.2014.04.048. PMID:24995984
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (299 Kb) [Save to disk]
  • Biological Unit Coordinates (4p5m.pdb1.gz) 77 Kb
  • Biological Unit Coordinates (4p5m.pdb2.gz) 77 Kb
  • Biological Unit Coordinates (4p5m.pdb3.gz) 76 Kb
  • Biological Unit Coordinates (4p5m.pdb4.gz) 76 Kb
  • LPC: Ligand-Protein Contacts for 4P5M
  • CSU: Contacts of Structural Units for 4P5M
  • Structure Factors (4134 Kb)
  • Retrieve 4P5M in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4P5M from S2C, [Save to disk]
  • Re-refined 4p5m structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 4P5M 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 4P5M
  • 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 4P5M, from MSDmotif at EBI
  • Fold representative 4p5m from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4p5m_H] [4p5m_D] [4p5m_A] [4p5m_C] [4p5m_G] [4p5m] [4p5m_E] [4p5m_F] [4p5m_B]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 4P5M: [IGc1] [MHC_II_alpha] [MHC_II_beta ] by SMART
  • Other resources with information on 4P5M
  • Community annotation for 4P5M at PDBWiki (http://pdbwiki.org)

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