OCA Atlas for 1AGC
1AGC Histocompatibility Complex date Mar 24, 1997
title Antagonist Hiv-1 Gag Peptides Induce Structural Changes In Hla B8 - Hiv-1 Gag Peptide (Ggkkkyql - 7q Mutation)
authors S.W.Reid, S.Mcadam, K.J.Smith, P.Klenerman, C.A.O'Callaghan, K.Harlos, B.K.Jakobsen, A.J.Mcmichael, J.I.Bell, D.I.Stuart, E.Y.Jones
compound source
Molecule: B0801
Chain: A
Fragment: Extracellular
Synonym: B8
Engineered: Yes
 Organism_scientific: Homo Sapiens
Organism_common: Human
Expression_system: Escherichia Coli
Expression_system_cell_line: Bl21(De3)Plyss
Expression_system_plasmid: Pgmt7

Molecule: Beta-2 Microglobulin
Chain: B
Fragment: Extracellular
Synonym: B2m
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Expression_system: Escherichia Coli
Expression_system_cell_line: Xa90
Expression_system_plasmid: Phn1

Molecule: Hiv-1 Gag Peptide (Ggkkkyql - 7q Mutation)
Chain: C
Fragment: Extracellular
Synonym: Peptide
Engineered: Yes
Synthetic: Naturally Occurring Biological Sequence
Organism_scientific: Homo Sapiens
Organism_common: Human
symmetry Space Group: P 21 21 21
R_factor 0.184
crystal
cell
length a length b length c angle alpha angle beta angle gamma
50.400 80.900 109.200 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.1 Å
related structures by homologous chain: 1AGD, 1AGF
similarity Contains 1 immunoglobulin-like domain.[MHC_I]
subunit Dimer of alpha chain and a beta chain (beta-2- microglobulin).
subcellular loc. Secreted.
genes B2M, HLA-B, HLAB (H. sapiens)
function Involved in the presentation of foreign antigens to the immune system. Beta-2-microglobulin is the beta-chain of major histocompatibility complex class i molecules.
disease Hemodialysis-related amyloidosis
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (84 Kb) [Save to disk]
  • CSU: Contacts of Structural Units for 1AGC
  • Likely Quarternary Molecular Structure file(s) for 1AGC
  • Retrieve 1AGC in mmCIF format [Save to disk]
    • View 1AGC in 3D
  • Protein Explorer, Easier to use and more powerful than RasMol. (Win and Mac only)
  • FirstGlance in Chemscape Chime (Install Chime freeware) This is good for easiest viewing of basic structure.
  • RasMol (Install RasMol freeware) Here's help on how to use RasMol.
    • Visual 3D analysis of 1AGC
  • STING, shows the sequence and maps the locations of sequence residues or residue ranges onto the 3D structure.
  • Noncovalent Bond Finder displays the closest contacts to ligand or interface, reports distances, walks over water bridges.
  • GRASS (Graphical Representation and Analysis of Structure Server)
    • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Genome occurence of 1AGC's fold from GeneCensus
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1agca2, region A:1-181 [rasmolscript] [script source]
        - Domain d1agca1, region A:182-276 [rasmolscript] [script source]
        - Domain d1agcb1, region B: [rasmolscript] [script source]
  • Fold representative 1agc from FSSP and Dali (Families of Structurally Similar Proteins)
  • Domain Definition for 1agc from 3Dee ( The Database of Protein Domain Definitions )
  • Class (fold), Architecture (subfold), Topology, Homologous superfamily: CATH
  • Summaries and structural analyses of PDB data files: PDBSum
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [1agc_A] [1agc_B] [1agc_C]
  • SWISS-PROT database: [B2MG_HUMAN] [1B04_HUMAN]
  • Domain organization of [B2MG_HUMAN] [1B04_HUMAN] by SWISSPFAM
  • Domain found in 1AGC: [IGc1 ] by SMART
  • Conserved protein region description, domain view and alignment from family MHC_I (PF00129) of Pfam.
  • Alignments of the sequence of 1AGC with the sequences similar proteins can be viewed for classification [B2MG_HUMAN] [1B04_HUMAN] 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 [B2MG_HUMAN] [1B04_HUMAN] at ProtoMap. Click on the Cluster number.
    • Other resources with information on 1AGC
  • InterPro: IPR003006 , IPR001039 , IPR003597
  • PDBREPORT (protein verification by WHAT_CHECK procedures)
  • MMDB (Entrez's Structure Database)
    • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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