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MSD motif www.ebi.ac.uk/msd-srv/msdmotif. 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 www ebi ac uk msd srv msdmotif

MSD motifwww.ebi.ac.uk/msd-srv/msdmotif

Structure Annotation

and

Function Assignment with MSDmotif

PDB: 1gci



Small motifs
Small motifs

Alpha-Beta Motif

Nest

ST staple

11 motifs in total

Prof James Milner-White


Small motif stats
Small motif stats

Occurrence of amino-acids

Correlation of side chain charge





Small motifs viewing
Small motifs viewing

Ligands

Catalytic sites

ProSite

Small motifs

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


Search
, search

PDB:1gci

Ideal for short loops search


Search continue
, search - continue

PDB:1gci

Subtilases family

PDB:1f5p

Globins family


Search vs sequence search
, search vs sequence search

Sequences found while search by , :

Subtilases family

NNSIGVL

DNTTGVL

DNSIGVL

Globins family

IVDTGSV

Blast search for

NNSIGVL

Diphtheria toxin family

SDSIGVL


3d motif research
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
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 search

ZN binding pattern: CXXCXXXFXXXXXLXXHXXXH



Sequence search
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
Helper application for multiple sequences alignment

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

Mime-type: application/x-blast

Blixem http://www.cgb.ki.se/cgb/groups/sonnhammer/Blixem.html


Helper application for multiple sequences alignment1
Helper application for multiple sequences alignment

Jalview as helper browser application for sequences alignment

Mime-type:

application/x-align

http://www.jalview.org/

Alignment of Zinc binding PROSITE patter hits


Sequence hits 3d alignment
Sequence hits 3D alignment

2 hits with less than 25% sequence identity

Fragments alignment

Chains alignment


Secondary structure patterns
Secondary structure patterns

Strand – turn – Strand

2-3 residues gap

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

Where N binds sugar: Man or Nag




Msd motif

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