OCA Atlas for 1FV1
1FV1 Immune System date Sep 18, 2000
title Structural Basis For The Binding Of An Immunodominant Peptide From Myelin Basic Protein In Different Registers By Two Hla-Dr2 Alleles
authors Y.Li, H.Li, R.Martin, A.R.Mariuzza
compound source
Molecule: Major Histocompatibility Complex Alpha Chain
Chain: A, D
Engineered: Yes
 Organism_scientific: Homo Sapiens
Organism_common: Human
Expression_system: Escherichia Coli
Expression_system_common: Bacteria

Molecule: Major Histocompatibility Complex Beta Chain
Chain: B, E
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Expression_system: Escherichia Coli
Expression_system_common: Bacteria

Molecule: Myelin Basic Protein
Chain: C, F
Fragment: Residues 86-105
Engineered: Yes
Synthetic: Yes
Other_details: The Peptide Was Chemically Synthesized. The Sequence Of The Peptide Is Naturally Found In Homo Sapiens (Human).
symmetry Space Group: P 1 21 1
R_factor 0.233
crystal
cell
length a length b length c angle alpha angle beta angle gamma
63.189 114.892 63.175 90.00 90.90 90.00
method X-Ray Diffractionresolution 1.90 Å
ligand SO4, CRYenzyme
related structures by homologous chain: 1D5Z
similarity Belongs to the MHC_II_alpha family.
gene HLA-DRA (H. sapiens)
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (158 Kb) [Save to disk]
  • LPC: Ligand-Protein Contacts for 1FV1
  • CSU: Contacts of Structural Units for 1FV1
  • Likely Quarternary Molecular Structure file(s) for 1FV1
  • Structure Factors (r1fv1sf.ent.Z) 486 Kb
  • Retrieve 1FV1 in mmCIF format [Save to disk]
    • View 1FV1 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 1FV1
  • 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 d1fv1a2, region A:3-81 [rasmolscript] [script source]
        - Domain d1fv1a1, region A:82-181 [rasmolscript] [script source]
        - Domain d1fv1b2, region B:1-92 [rasmolscript] [script source]
        - Domain d1fv1b1, region B:93-190 [rasmolscript] [script source]
        - Domain d1fv1d2, region D:4-81 [rasmolscript] [script source]
        - Domain d1fv1d1, region D:82-181 [rasmolscript] [script source]
        - Domain d1fv1e2, region E:1-92 [rasmolscript] [script source]
        - Domain d1fv1e1, region E:93-190 [rasmolscript] [script source]
  • Fold representative 1fv1 from FSSP and Dali (Families of Structurally Similar Proteins)
  • 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: [1fv1_F] [1fv1_A] [1fv1_B] [1fv1_C] [1fv1_D] [1fv1_E]
  • SWISS-PROT database: [HA2R_HUMAN]
  • Domain organization of [HA2R_HUMAN] by SWISSPFAM
  • Domain found in 1FV1: [IGc1 ] by SMART
  • Conserved protein region description, domain view and alignment from family MHC_II_alpha (PF00993) of Pfam.
  • Alignments of the sequence of 1FV1 with the sequences similar proteins can be viewed for classification [HA2R_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 [HA2R_HUMAN] at ProtoMap. Click on the Cluster number.
    • Other resources with information on 1FV1
  • InterPro: IPR003006 , IPR003597 , IPR001003
  • 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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