1KG0	Viral Protein Immune System	date	Nov 25, 2001
title	Structure Of The Epstein-Barr Virus Gp42 Protein Bound To The Mhc Class II Receptor Hla-Dr1
authors	M.M.Mullen, K.M.Haan, R.Longnecker, T.S.Jardetzky
compound		source
Molecule: Mhc Class II Receptor Hla-Dr1 Chain: A Fragment: Alpha Chain, Extracellular Domain Engineered: Yes		Organism_scientific: Homo Sapiens Organism_common: Human Organism_taxid: 9606 Expression_system: Escherichia Coli Expression_system_taxid: 562
Molecule: Mhc Class II Receptor Hla-Dr1 Chain: B Fragment: Beta Chain, Extracellular Domain Engineered: Yes		Organism_scientific: Homo Sapiens Organism_common: Human Organism_taxid: 9606 Expression_system: Escherichia Coli Expression_system_taxid: 562
Molecule: Hemagglutinin Ha Peptide Chain: D Fragment: Antigenic Peptide Engineered: Yes		Synthetic: Yes Other_details: Synthetic Peptide Derived From Influenza Hemagglutinin Sequence;
Molecule: Gp42 Protein Chain: C Fragment: Extracellular Domain Engineered: Yes		Organism_scientific: Human Herpesvirus 4 Organism_common: Epstein-Barr Virus Organism_taxid: 10376 Strain: Gd1 Expression_system: Trichoplusia Ni Expression_system_common: Cabbage Looper Expression_system_taxid: 7111 Expression_system_vector_type: Baculovirus Expression_system_plasmid: Pbac-Gus3
symmetry	Space Group: P 63 2 2	R_factor 0.221 R_Free 0.247
crystal cell	length a length b length c angle alpha angle beta angle gamma 170.400 170.400 101.000 90.00 90.00 120.00
method	X-Ray Diffraction	resolution	2.65 Å
related structures	by homologous chain: 1IAO, 1JWM, 1R5I
Primary reference	Structure of the Epstein-Barr virus gp42 protein bound to the MHC class II receptor HLA-DR1., Mullen MM, Haan KM, Longnecker R, Jardetzky TS, Mol Cell 2002 Feb;9(2):375-85. PMID:11864610

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (105 Kb) [Save to disk] Biological Unit Coordinates (1kg0.pdb1.gz) 100 Kb CSU: Contacts of Structural Units for 1KG0 Likely Quarternary Molecular Structure file(s) for 1KG0 Retrieve 1KG0 in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 1KG0 from S2C, [Save to disk]

View 1KG0 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. On AstexViewer, from MSD-EBI (viewer documentation). On RasMol (Install RasMol freeware) Here's help on how to use RasMol.

Visual 3D analysis of 1KG0

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 1KG0, from MSDmotif at EBI Classification of representative domains in scop (Structural Classification of Proteins)     - Domain d1kg0a2, region A:3-81 [Jmol] [rasmolscript] [script source]     - Domain d1kg0a1, region A:82-182 [Jmol] [rasmolscript] [script source]     - Domain d1kg0b2, region B:3-92 [Jmol] [rasmolscript] [script source]     - Domain d1kg0b1, region B:93-190 [Jmol] [rasmolscript] [script source]     - Domain d1kg0c_, region C [Jmol] [rasmolscript] [script source] Fold representative 1kg0 from FSSP and Dali (Families of Structurally Similar Proteins) Class (fold), Architecture (subfold), Topology, Homologous superfamily from CATH Summaries and structural analyses of PDB data files from PDBSum Identification of Protein Pockets & Cavities at CASTp

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [1kg0_A] [1kg0_B] [1kg0_C] [1kg0_D] SWISS-PROT database: [P04229] [P01903] [P03205] Domain organization of [2B11_HUMAN] [DRA_HUMAN] [GP42_EBVB9] by SWISSPFAM Domains found in 1KG0: [CLECT] [IGc1] [MHC_II_alpha] [MHC_II_beta ] by SMART Alignments of the sequence of 1KG0 with the sequences similar proteins can be viewed for 1KG0's classification [2B11_HUMAN] [DRA_HUMAN] [GP42_EBVB9] 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 [2B11_HUMAN] [DRA_HUMAN] [GP42_EBVB9] at ProtoMap. Click on the Cluster number.

Other resources with information on 1KG0

Community annotation for 1KG0 at PDBWiki (http://pdbwiki.org) MMDB (Entrez's Structure Database)

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