1SJH	Immune System	date	Mar 03, 2004
title	Hla-Dr1 Complexed With A 13 Residue Hiv Capsid Peptide
authors	Z.Zavala-Ruiz, I.Strug, B.D.Walker, P.J.Norris, L.J.Stern
compound		source
Molecule: Hla Class II Histocompatibility Antigen, Dr Alpha Chain; Chain: A Fragment: Extracellular Domain Of Hla-Dra0101 Synonym: Mhc Class II Antigen Dra Engineered: Yes		Organism_scientific: Homo Sapiens Organism_common: Human Organism_taxid: 9606 Gene: Hla-Dra Expression_system: Escherichia Coli Bl21(De3) Expression_system_taxid: 469008 Expression_system_strain: Bl21(De3) Expression_system_vector_type: T7 Polymeraselac Expression_system_plasmid: Plm1
Molecule: Hla Class II Histocompatibility Antigen, Drb1-1 Beta Chain; Chain: B Fragment: Extracellular Domain Of Hla-Drb0101 Synonym: Mhc Class I Antigen Drb11, Dr-1, Dr1 Engineered: Yes		Organism_scientific: Homo Sapiens Organism_common: Human Organism_taxid: 9606 Gene: Hla-Drb1 Expression_system: Escherichia Coli Bl21(De3) Expression_system_taxid: 469008 Expression_system_strain: Bl21(De3) Expression_system_vector_type: T7 Polymeraselac Expression_system_plasmid: Plm1
Molecule: Gag Polyprotein Chain: C Fragment: 13 Residue Peptide From Hiv-1 Gag Capsid Protein Engineered: Yes		Synthetic: Yes Other_details: Synthesized Peptide With Sequence From Human Immunodeficiency Virus Type 1 (Hiv-1) Gag Capsid Protein [166-178];
Molecule: Enterotoxin Type C-3 Chain: D Fragment: Sec3 Variant 3b2 Synonym: Sec3 Engineered: Yes Mutation: Yes		Organism_scientific: Staphylococcus Aureus Organism_taxid: 1280 Gene: Entc3, Sav2009, Sa1817 Expression_system: Escherichia Coli Expression_system_taxid: 562 Expression_system_strain: Hb2151 Expression_system_vector_type: Lac
symmetry	Space Group: H 3	R_factor 0.220 R_Free 0.245
crystal cell	length a length b length c angle alpha angle beta angle gamma 172.464 172.464 121.461 90.00 90.00 120.00
method	X-Ray Diffraction	resolution	2.25 Å
related structures	by homologous chain: 1I4Q, 1JWU, 1PYW, 1S9V
Gene Ontology	Chain Function Process Component D pathogenesis extracellular region
Primary reference	A hairpin turn in a class II MHC-bound peptide orients residues outside the binding groove for T cell recognition., Zavala-Ruiz Z, Strug I, Walker BD, Norris PJ, Stern LJ, Proc Natl Acad Sci U S A 2004 Sep 7;101(36):13279-84. Epub 2004 Aug 26. PMID:15331779

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (113 Kb) [Save to disk] Biological Unit Coordinates (1sjh.pdb1.gz) 318 Kb CSU: Contacts of Structural Units for 1SJH Likely Quarternary Molecular Structure file(s) for 1SJH Structure Factors (521 Kb) Retrieve 1SJH in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 1SJH from S2C, [Save to disk] Re-refined 1sjh structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 1SJH 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 1SJH

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 1SJH, from MSDmotif at EBI Classification of representative domains in scop (Structural Classification of Proteins)     - Domain d1sjha2, region A:4-81 [Jmol] [rasmolscript] [script source]     - Domain d1sjha1, region A:82-181 [Jmol] [rasmolscript] [script source]     - Domain d1sjhb2, region B:1-92 [Jmol] [rasmolscript] [script source]     - Domain d1sjhb1, region B:93-190 [Jmol] [rasmolscript] [script source]     - Domain d1sjhd1, region D:1-121 [Jmol] [rasmolscript] [script source]     - Domain d1sjhd2, region D:122-239 [Jmol] [rasmolscript] [script source] Fold representative 1sjh 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: [1sjh_A] [1sjh_B] [1sjh_C] [1sjh_D] SWISS-PROT database: [P04229] [P01903] [P0A0L5] [P12495] Domain organization of [2B11_HUMAN] [DRA_HUMAN] [ENTC3_STAAU] [GAG_HV1Z2] by SWISSPFAM Domains found in 1SJH: [IGc1] [MHC_II_alpha] [MHC_II_beta ] by SMART Alignments of the sequence of 1SJH with the sequences similar proteins can be viewed for 1SJH's classification [2B11_HUMAN] [DRA_HUMAN] [ENTC3_STAAU] [GAG_HV1Z2] 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] [ENTC3_STAAU] [GAG_HV1Z2] at ProtoMap. Click on the Cluster number.

Other resources with information on 1SJH

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

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