3BGM	Immune System	date	Nov 27, 2007
title	Crystal Structure Of Pkd2 Phosphopeptide Bound To Human Class I Mhc Hla-A2
authors	F.Mohammed, M.Cobbold, A.L.Zarling, M.Salim, G.A.Barrett-Wilt, J.Shabanowitz, D.F.Hunt, V.H.Engelhard, B.E.Willcox
compound		source
Molecule: Hla Class I Histocompatibility Antigen, A-2 Alpha Chain; Chain: A Fragment: Alpha-1, Alpha-2, Alpha-3 Synonym: Mhc Class I Antigen A2 Engineered: Yes		Organism_scientific: Homo Sapiens Organism_common: Human Organism_taxid: 9606 Gene: Hla-A, Hlaa Expression_system: Escherichia Coli Expression_system_taxid: 562 Expression_system_strain: Bl21(De3)Plyss Expression_system_vector_type: Plasmid Expression_system_plasmid: Pgmt7
Molecule: Beta-2-Microglobulin Chain: B Engineered: Yes		Organism_scientific: Homo Sapiens Organism_common: Human Organism_taxid: 9606 Gene: B2m Expression_system: Escherichia Coli Expression_system_taxid: 562 Expression_system_strain: Bl21(De3)Plyss Expression_system_vector_type: Plasmid Expression_system_plasmid: Pgmt7
Molecule: Nonameric Peptide From Serinethreonine-Protein Kinase D2; Chain: C Fragment: Unp Residues 526-534 Synonym: Npkc-D2 Engineered: Yes		Synthetic: Yes Other_details: Commercial Synthesis
symmetry	Space Group: C 1 2 1	R_factor 0.202 R_Free 0.232
crystal cell	length a length b length c angle alpha angle beta angle gamma 117.800 54.800 75.800 90.00 105.00 90.00
method	X-Ray Diffraction	resolution	1.60 Å
ligand	EDO, SEP	enzyme
Gene Ontology	Chain Function Process Component B cellular response to iron io...
Primary reference	Phosphorylation-dependent interaction between antigenic peptides and MHC class I: a molecular basis for the presentation of transformed self., Mohammed F, Cobbold M, Zarling AL, Salim M, Barrett-Wilt GA, Shabanowitz J, Hunt DF, Engelhard VH, Willcox BE, Nat Immunol. 2008 Nov;9(11):1236-43. Epub 2008 Oct 5. PMID:18836451

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (77 Kb) [Save to disk] Biological Unit Coordinates (3bgm.pdb1.gz) 72 Kb LPC: Ligand-Protein Contacts for 3BGM CSU: Contacts of Structural Units for 3BGM Likely Quarternary Molecular Structure file(s) for 3BGM Structure Factors (908 Kb) Retrieve 3BGM in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 3BGM from S2C, [Save to disk] Re-refined 3bgm structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 3BGM 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 3BGM

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 3D motif for 3BGM, from MSDmotif at EBI

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [3bgm_A] [3bgm_C] [3bgm] [3bgm_B] SWISS-PROT database: [P01892] [P61769] [Q9BZL6] Domain organization of [1A02_HUMAN] [B2MG_HUMAN] [KPCD2_HUMAN] by SWISSPFAM Domain found in 3BGM: [IGc1 ] by SMART

Other resources with information on 3BGM

Community annotation for 3BGM at PDBWiki (http://pdbwiki.org) MMDB (Entrez's Structure Database)

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