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MSD motif PowerPoint PPT Presentation

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MSD motif Structure Annotation and Function Assignment with MSDmotif. PDB: 1gci. MSDmotif front options. Small motifs. Alpha-Beta Motif. Nest. ST staple. 11 motifs in total Prof James Milner-White. Small motif stats. Occurrence of amino-acids.

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MSD motif

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Structure Annotation


Function Assignment with MSDmotif

PDB: 1gci

MSDmotif front options

Small motifs

Alpha-Beta Motif


ST staple

11 motifs in total

Prof James Milner-White

Small motif stats

Occurrence of amino-acids

Correlation of side chain charge

Small motif stats

Small motifs – hit list from stats

Small motifs – 3D alignment


Small motifs viewing


Catalytic sites


Small motifs

“Group” menu item contains a list of presented in a PDB entry sites and motifs

, search


Ideal for short loops search

, search - continue


Subtilases family


Globins family

, search vs sequence search

Sequences found while search by , :

Subtilases family




Globins family


Blast search for


Diphtheria toxin family


3D motif research

Asx turn

PDB 1e4m has the small motif - Asx turn of residues 65-67 (ASP-HIS-GLY), which is found in a loop between two helixes

Use phi/psi parameters of these three residues for a search

3D motif research - continue

  • The sequences from the hit list:

    • LKY

    • QGF

    • DRF

    • AGV

    • RGV

    • DHG

    • MGK

    • DNL

    • HGV

    • ANN

    • TGA

    • QCY

    • LGA

    • NSY

Most of these hits were found in loops between helixes

Pattern search


Pattern hits 3D alignment

Sequence search

  • Pseudo multiple sequence alignment (blast output based)

  • Ligand binding residues are marked

  • Normalization of hit list to 50% sequence identity

Helper application for multiple sequences alignment

Blixem as helper browser application for multiple sequences alignment based on blast output

Mime-type: application/x-blast


Helper application for multiple sequences alignment

Jalview as helper browser application for sequences alignment



Alignment of Zinc binding PROSITE patter hits

Sequence hits 3D alignment

2 hits with less than 25% sequence identity

Fragments alignment

Chains alignment

Secondary structure patterns

Strand – turn – Strand

2-3 residues gap

Glycosylation pattern N{P}[ST]{P}

Where N binds sugar: Man or Nag

Secondary structure patterns - continue

Secondary structure patterns - continue

MSD motif

Small 3D motifs from J.Milner-White search/view

Secondary structure patterns (HTH) search/view

,, based search/view

Ligands and their environment search/view

Catalytic sites search/view

Blast sequence search/view

PROSITE format compliant patterns search/view

3D and sequence multiple alignment

Hit list and statistics normalization by SCOP,CATH

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