3PGD Immune System date Nov 01, 2010
title Crystal Structure Of Hla-Dr1 With Clip106-120, Canonical Pep Orientation
authors S.Gunther, A.Schlundt, J.Sticht, Y.Roske, U.Heinemann, K.H.Wiesm G.Jung, K.Falk, O.Rotzschke, C.Freund
compound source
Molecule: Hla Class II Histocompatibility Antigen, Dr Alpha
Chain: A, D
Fragment: Unp Residues 26-217
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: Escherichia Coli
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet11a

Molecule: Hla Class II Histocompatibility Antigen, Drb1-1 B
Chain: B, E
Fragment: Unp Residues 30-227
Synonym: Mhc Class II Antigen Drb11, Dr-1, Dr1
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Hla-Drb1
Expression_system: Escherichia Coli
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet24d

Molecule: Hla Class II Histocompatibility Antigen Gamma Cha
Chain: C, F
Fragment: Unp Residues 106-120
Synonym: Hla-Dr Antigens-Associated Invariant Chain, Ia Ant Associated Invariant Chain, II, P33;
Engineered: Yes

Synthetic: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
symmetry Space Group: P 43 21 2
R_factor 0.196 R_Free 0.242
crystal
cell
length a length b length c angle alpha angle beta angle gamma
94.449 94.449 275.535 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.72 Å
Primary referenceBidirectional binding of invariant chain peptides to an MHC class II molecule., Gunther S, Schlundt A, Sticht J, Roske Y, Heinemann U, Wiesmuller KH, Jung G, Falk K, Rotzschke O, Freund C, Proc Natl Acad Sci U S A. 2010 Nov 29. PMID:21115828
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (135 Kb) [Save to disk]
  • Biological Unit Coordinates (3pgd.pdb1.gz) 66 Kb
  • Biological Unit Coordinates (3pgd.pdb2.gz) 67 Kb
  • CSU: Contacts of Structural Units for 3PGD
  • Structure Factors (278 Kb)
  • Retrieve 3PGD in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3PGD from S2C, [Save to disk]
  • Re-refined 3pgd structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3PGD 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 3PGD
  • 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 3PGD, from MSDmotif at EBI
  • Fold representative 3pgd from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3pgd_E] [3pgd] [3pgd_A] [3pgd_B] [3pgd_C] [3pgd_D] [3pgd_F]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 3PGD: [IGc1] [MHC_II_alpha] [MHC_II_beta ] by SMART
  • Other resources with information on 3PGD
  • Community annotation for 3PGD 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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