Thornton Group databases

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Thornton Group databases
Roman Laskowski, EBI
Protein-Protein interaction server
Protein-DNA interaction server
DNA-binding protein structural families
Scorecons
http//www.ebi.ac.uk/Thornton/databases.html
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PDBsum A database of the known 3D structures of
proteins and nucleic acids
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Example PDBsum page
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Protein page
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Residue conservation
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Protein page again
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SAS hits for 1bpy
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SAS annotations
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SAS home page
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DNA page
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Ligand page
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Enzyme reaction
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Enzyme Structures Database
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EC 1.1.1.1
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PDBsum home again
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Species page
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PDBsum home again
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Highlights page
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Smallest structures page
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1tn1 page
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Catalytic site atlas home page
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CSA entry
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CSA entry II
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CSA partial search
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MSA home page
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MSA entry
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Pita home page
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Pita results for 1sip
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Other databases
Protein-Protein interaction server
Protein-DNA interaction server
DNA-binding protein structural families
Scorecons
Sidechain-sidechain interactions
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ProFunc home page
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SG structures of unknown function in the PDB

• Hypothetical protein Af0491 from A. fulgidus

• Ubiquitin-like domain from mouse

• Signalling protein from sheep

• Putative serine hydrolase from S.cerevisiae

• Predicted glutamine amidotransferase from P.
  aeruginosa

• Probable eukaryotic D-amino acid tRNA deacetylase

• Molybdenum cofactor biosynthetic enzyme

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Predicting function from 3D structure
A L Y F G H I L V Y S T F P N E E K A L E I G R K
L L E K R L I A C F N A F E I R S G Y W W K G E I
V Q D K E W A A I F K T T E E K E K E L Y E E L R
K L H P Y E T P A I F T L K V E N I L T E Y N W L
R E S V L G S
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Predicting function from 3D structure
A L Y F G H I L V Y S T F P N E E K A L E I G R K
L L E K R L I A C F N A F E I R S G Y W W K G E I
V Q D K E W A A I F K T T E E K E K E L Y E E L R
K L H P Y E T P A I F T L K V E N I L T E Y N W L
R E S V L G S
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ProFunc
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Template methods
eg 189 enzyme active site templates

Carbamoylsarcosine amidohhydrase
Ser-His-Asp catalytic triad
Dihydrofolate reductase
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Automatically generated templates
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Reverse templates (SiteSeer)
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Scoring template matches
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Scoring template matches
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Scoring template matches
Similar residues in neighbourhood
Template structure 1mbb
Query structure 1hsk
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An examplechitinase A and B from S.marcescens
Sequence identity of 28.7 (in 428 a.a. o/lap)
So, function likely to be different
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Chitinase A
Chitinase A is an enzyme (E.C.3.2.1.14)
breaks chitin into its constituent GlcNac
residues
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Chitinase B
Chitinase B matches E.C.3.2.1.14 template
with a high site similarity score
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Superposition of chitinase A and B