3PDO Immune System date Oct 23, 2010
title Crystal Structure Of Hla-Dr1 With Clip102-120
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
Fragment: Extracellular Domain
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
Fragment: Extracellular Domain
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
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 21 21 21
R_factor 0.191 R_Free 0.240
crystal
cell
length a length b length c angle alpha angle beta angle gamma
45.450 97.627 99.052 90.00 90.00 90.00
method X-Ray Diffractionresolution 1.95 Å
ligand FMT, GOL enzyme
Gene
Ontology
ChainFunctionProcessComponent
A


B


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] (77 Kb) [Save to disk]
  • Biological Unit Coordinates (3pdo.pdb1.gz) 73 Kb
  • LPC: Ligand-Protein Contacts for 3PDO
  • CSU: Contacts of Structural Units for 3PDO
  • Structure Factors (482 Kb)
  • Retrieve 3PDO in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3PDO from S2C, [Save to disk]
  • Re-refined 3pdo structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3PDO 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 3PDO
  • 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 3PDO, from MSDmotif at EBI
  • Fold representative 3pdo from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3pdo_C] [3pdo_A] [3pdo_B] [3pdo]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 3PDO: [IGc1] [MHC_II_alpha] [MHC_II_beta ] by SMART
  • Alignments of the sequence of 3PDO with the sequences similar proteins can be viewed for 3PDO's classification at ProtoMap. Click on "Neighbors List", then on the "See Alignments" button below the list.
  • A sequence distance tree ("phylogenetic tree") can be viewed for 1ACL's classification at ProtoMap. Click on the Cluster number.
  • Other resources with information on 3PDO
  • Community annotation for 3PDO at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
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