OCA Atlas for 1F3J
1F3J Immune System date Jun 04, 2000
title Histocompatibility Antigen I-Ag7
authors R.R.Latek, A.Suri, S.J.Petzold, C.A.Nelson, O.Kanagawa, E.R.Unanue, D.H.Fremont
compound source
Molecule: H-2 Class II Histocompatibility Antigen
Chain: A, D
Fragment: A-D Alpha Chain
Engineered: Yes
 Organism_scientific: Mus Musculus
Organism_common: Mouse
Expression_system: Spodoptera Frugiperda
Expression_system_common: Fall Armyworm
Expression_system_vector: Baculovirus

Molecule: Mhc Class II Nod
Chain: B, E
Fragment: Beta Chain
Engineered: Yes
Organism_scientific: Mus Musculus
Organism_common: Mouse
Expression_system: Spodoptera Frugiperda
Expression_system_common: Fall Armyworm
Expression_system_vector: Baculovirus

Molecule: Lysozyme C
Chain: P, Q
Fragment: Residues 11-24, Correspond To Binding Sites P-3 To P11;
Engineered: Yes
Organism_scientific: Gallus Gallus
Organism_common: Chicken
Expression_system: Spodoptera Frugiperda
Expression_system_common: Fall Armyworm
Expression_system_vector: Baculovirus
symmetry Space Group: P 41 21 2
R_factor 0.221
crystal
cell
length a length b length c angle alpha angle beta angle gamma
109.540 109.540 176.360 90.00 90.00 90.00
method X-Ray Diffractionresolution 3.10 Å
ligand NAGenzyme
similarity Belongs to family 22 of glycosyl hydrolases.[lys]
subunit Monomer.
catalytic activ. Hydrolysis of the 1,4-beta-linkages between n- acetyl-d-glucosamine and n-acetylmuramic acid in peptidoglycan heteropolymers of the prokaryotes cell walls.
tissue In the egg white and polymorphonuclear leukocytes.
function Lysozymes have primarily bacteriolytic function; those in tissues and body fluids are associated with the monocyte- macrophage system and enhance the activity of immunoagents.
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (153 Kb) [Save to disk]
  • LPC: Ligand-Protein Contacts for 1F3J
  • CSU: Contacts of Structural Units for 1F3J
  • Likely Quarternary Molecular Structure file(s) for 1F3J
  • Retrieve 1F3J in mmCIF format [Save to disk]
    • View 1F3J 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 1F3J
  • 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.
    • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1f3ja2, region A:1-82 [rasmolscript] [script source]
        - Domain d1f3ja1, region A:83-181 [rasmolscript] [script source]
        - Domain d1f3jb2, region B:4-93 [rasmolscript] [script source]
        - Domain d1f3jb1, region B:94-191 [rasmolscript] [script source]
        - Domain d1f3jd2, region D:1-82 [rasmolscript] [script source]
        - Domain d1f3jd1, region D:83-181 [rasmolscript] [script source]
        - Domain d1f3je2, region E:4-93 [rasmolscript] [script source]
        - Domain d1f3je1, region E:94-191 [rasmolscript] [script source]
  • Fold representative 1f3j from FSSP and Dali (Families of Structurally Similar Proteins)
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [1f3j_P] [1f3j_Q] [1f3j_A] [1f3j_B] [1f3j_D] [1f3j_E]
  • SWISS-PROT database: [LYC_CHICK]
  • Domain organization of [LYC_CHICK] by SWISSPFAM
  • Domain found in 1F3J: [IGc1 ] by SMART
  • Conserved protein region description, domain view and alignment from family lys (PF00062) of Pfam.
  • Alignments of the sequence of 1F3J with the sequences similar proteins can be viewed for classification [LYC_CHICK] 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 [LYC_CHICK] at ProtoMap. Click on the Cluster number.
    • Other resources with information on 1F3J
  • InterPro: IPR001916
  • 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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