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

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MSD motifwww.ebi.ac.uk/msd-srv/msdmotif
Structure Annotation and Function Assignment
with MSDmotif
PDB 1gci
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MSDmotif front options
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Small motifs
Alpha-Beta Motif
Nest
ST staple
11 motifs in total Prof James Milner-White
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Small motif stats
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Small motif stats
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Small motifs hit list from stats
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Small motifs 3D alignment
ST-staple
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Small motifs viewing
Group menu item contains a list of presented in
a PDB entry sites and motifs
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?,? search
PDB1gci
Ideal for short loops search
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?,? search - continue
PDB1gci Subtilases family
PDB1f5p Globins family
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?,? 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
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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
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3D motif research - continue
The sequences from the hit list LKY QGF DRF AGV R
GV DHG MGK DNL HGV ANN TGA QCY LGA NSY
Most of these hits were found in loops between
helixes
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Pattern search
ZN binding pattern CXXCXXXFXXXXXLXXHXXXH
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Pattern hits 3D alignment
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Sequence search

• Pseudo multiple sequence alignment (blast output
  based)
• Ligand binding residues are marked
• Normalization of hit list to 50 sequence
  identity

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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
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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
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Sequence hits 3D alignment
2 hits with less than 25 sequence identity
Fragments alignment
Chains alignment
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Secondary structure patterns
Where N binds sugar Man or Nag
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Secondary structure patterns - continue
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Secondary structure patterns - continue
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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