1SM3 Complex (Antibody Peptide Epitope) date Dec 23, 1997
title Crystal Structure Of The Tumor Specific Antibody Sm3 Complex Peptide Epitope
authors P.Dokurno, P.A.Bates, H.A.Band, L.M.D.Stewart, J.M.Lally, J.M.Bur J.Taylor-Papadimitriou, M.J.E.Sternberg, D.Snary, P.S.Freemont
compound source
Molecule: Sm3 Antibody
Chain: L
Fragment: Fab Fragment
 Organism_scientific: Mus Musculus
Organism_common: House Mouse
Organism_taxid: 10090
Organ: Breast
Tissue: Epithelial

Molecule: Sm3 Antibody
Chain: H
Fragment: Fab Fragment
Organism_scientific: Mus Musculus
Organism_common: House Mouse
Organism_taxid: 10090
Organ: Breast
Tissue: Epithelial

Molecule: Peptide Epitope
Chain: P
Engineered: Yes
Other_details: Anti-Breast Tumour Antibody Sm3 Against Epit Mucin Muc1
symmetry Space Group: P 1 21 1
R_factor 0.213 R_Free 0.283
crystal
cell
length a length b length c angle alpha angle beta angle gamma
42.200 83.730 67.240 90.00 93.30 90.00
method X-Ray Diffractionresolution 1.95 Å
ligand CD, CL enzyme
related structures by homologous chain: 1A6V, 1GPO, 1MFE, 1QKZ
Gene
Ontology
ChainFunctionProcessComponent
L


Primary referenceCrystal structure at 1.95 A resolution of the breast tumour-specific antibody SM3 complexed with its peptide epitope reveals novel hypervariable loop recognition., Dokurno P, Bates PA, Band HA, Stewart LM, Lally JM, Burchell JM, Taylor-Papadimitriou J, Snary D, Sternberg MJ, Freemont PS, J Mol Biol 1998 Dec 4;284(3):713-28. PMID:9826510
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (78 Kb) [Save to disk]
  • Biological Unit Coordinates (1sm3.pdb1.gz) 72 Kb
  • LPC: Ligand-Protein Contacts for 1SM3
  • CSU: Contacts of Structural Units for 1SM3
  • Likely Quarternary Molecular Structure file(s) for 1SM3
  • Retrieve 1SM3 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1SM3 from S2C, [Save to disk]
    • View 1SM3 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.
    • Visual 3D analysis of 1SM3
  • Ramachandran plot from PDBSum
    • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • 3D motif for 1SM3, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1sm3h1, region H:1-113 [Jmol] [rasmolscript] [script source]
        - Domain d1sm3h2, region H:114-213 [Jmol] [rasmolscript] [script source]
        - Domain d1sm3l2, region L:108-208 [Jmol] [rasmolscript] [script source]
        - Domain d1sm3l1, region L:3-107 [Jmol] [rasmolscript] [script source]
  • 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: [1sm3_P] [1sm3_L] [1sm3_H] [1sm3]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 1SM3: [IG_like] [IGv ] by SMART
    • Other resources with information on 1SM3
  • Community annotation for 1SM3 at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
    • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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