How to query 3DID
The 3D structures of domain-motifs interactions
currently stored in 3did are described in the following publication:
Contextual Specificity in Peptide-Mediated Protein Interactions, Stein & Aloy, PLoS ONE 3(7): e2524, 2008.
- Enter a GO accession
code, and you'll get this GO term's name, all its ancestors and direct
children, plus PDB Chains and domains annotated with this term.
- If you don't know the exact GO term, give a keyword
to get a list of all the GO terms containing your keyword. Optionally, the
domains and/or Proteins (PDB chains) in 3DID annotated with this GO term are
counted. Note that counting the PDB Chains may take quite long, thus it is
recommended to check "Display only GO terms with Domains in 3DID"
as well to restrict the list length.
SCOP class based
- The SCOP query takes a SCOP classification value and returns all interactions with domains annotated with this value, if any.
Information on 3DID Output Pages
Domain and Motif View
The information on selected domain or motif is displayed
in smilar ways. The most important items are illustrated here:
|The domain name
|Global binding interfaces of the
query domain, visualizing the residues involved in this interaction interface, a link to each interaction domain
or motif, and links to the respective interactions
|A link to the Pfam entry
|A menu with GO terms for this domain, if any
|A menu with PDB chains containing this domain
|A network containing interacting
domains (in ellipses) and motifs (in rectangles) related to the domain or
motif queried for (in a diamond), and, depending on the network depth, their
interaction partners (details
Domain-Domain Interaction View
Besides some general information on the interaction, the page shows the following tables:
|Topologies observed for
this interaction, via residues from both domains that form the interface,
along with the frequency of this topology and a numeric identifier ("X : Y")
|# Cases ||Topology ||Interface Residues in Cyclin_C ||Interface Residues in Pkinase|
|84 ||1 :
|1 ||0 : 2 ||
|PDB examples of this domain-domain interaction
||chain 1 ||residues
||chain 2 ||residues
||2 : 2
||2 : 0
|The topology is shown using the
numeric identifiers established above. The identifiers link back to the
topology table, where you can see which residues of which domain are
A Jmol script visualizes the interaction;
participating residues are highlighted.
The "PDB ID" entries link to the Protein Databank, while
"more interactions" leads to the 3DID page for this PDB
|The table also contains links to our tool for plotting similarity in interactions (SimInt). SimInt plots structural comparisons (iRMSD) of all instances of interactions of known 3D structure, highlighting those between the domains of interest. This plot provides details as to how interactions involving particular families, superfamilies and folds, as defined in SCOP can vary. Based on an analysis of hundreds of interactions, we suggested that two pairs of proteins do interact in a similar way if the iRMSD is below 10Å.|
|Method ||Protein 1 ||domain ||Protein 2 ||domain|
|| 8-295 (pkinase)
||YFL029C || 27-230 (pkinase)
|Such an "Experimental Information" entry means that an interaction of these two proteins has been observed experimentally, and that the two domains from your query are contained in the two proteins, respectively. Hence it is possible that the interaction happens between these two domains, but it is not granted.|
Domain-Motif Interaction View
This page displays the motif pattern, which is recognized
by the domain, and its source database, followed by topologies and interaction
|Topologies observed for
this interaction, showing residues from the domain that form the interface,
along with the frequency of this topology and a numeric identifier
|# Cases ||Topology ||Interface Residues in RB_B|
|2 ||0 ||
|Detailed description of
this domain-motif interaction in 3D structures, with domain and motif position,
motif sequence, the number of contextual residues (residues that contact the
domain but lie outside the motif), and visualization of the interaction using Jmol.||
||domain chain ||residues
||motif chain ||residues
The interface visualization indicates which residues of a domain are used
in an interaction. The interface residues are clustered for all cases of
each interaction type, thus if more than one topology is shown,
multiple interaction topologies can be observed in the 3D structures of
In the domain view, global binding interfaces are shown, along with all
binding partners that interact here. The bar height indicates how many
partners actually use this residue in the interface.
The visualization uses a "rainbow" colorscheme, i.e., N-terminal residues
are in blue, then cyan, green, yellow, orange, and red at the C-terminus.
The path-finding algorithm is based on Breath-First-Search, thus all edges (=interactions) are weighted equally. If there is some path between your domains, all possible pathes of minimum length will be displayed as text and in a graph. In addition, there may be experimental information on a possible interaction of these two domains.
The PDB-graph contains all chains of this PDB that are referenced in 3DID
plus their domains (ellipses) and motifs (boxes). Chains that contain the
same domains are grouped into one block. Lines connecting the domains show
both inter- and intrachain interactions.
In the example on the right, Chain
A of 1gh6 contains the domain DnaJ and the motif LIG_RB_B, and Chain B
contains the domains RB_A and RB_B.
Domains and motifs are displayed at their respective positions in the
protein, linked to the corresponding 3DID pages. A thin black line
indicates that there is no PfamA domain in this position. If there are
overlapping domains or motifs, they are displayed in on an additional,
thinner line below.
The domain color is randomly chosen, but then consequently used on one page. The legend gives detailed information about the domain position.
|| (overlapping domains or motifs)
Ellipses in networks represent for domains, while boxes represent linear
motifs. Diamond shapes are used for the source domain (the one from which the
network is built) and also for the target domain in path queries.
By default, the interaction graph is colored randomly, but you can choose a
color scheme based on GO terms. The terms used for coloring are from level 3 of
the GO hierarchy, i.e., direct children of molecular_function,
biological_process, or cellular_component, respectively. If a domain is
annotated with a GO term on a more detailed level, its ancestors are traced up
to level 3. In case there are several possible terms, one is chosen
randomly. Since this data is precomputed, the level-3-terms won't change (at
least not until the next release).
The line style in the graph gives some information about the corresponding
interaction examples from the PDB: bold lines mean that this interaction has
only been seen intra-chain, thin lines stand for interchain interaction
only. If both inter- and intrachain interactions have been seen, the line
between the domains is dashed.