Getting Started

How to query 3DID

Domain-based

• To retrieve information on a domain, use the Domain Query. You can give the exact domain name, or use the wildcard character %. If no exact match is found, 3did will return a list of similar domain names. For exact matches, the results will provide Domain Information for each domain in 3DID that matches your input. If you have the Pfam access code for your domain of interest, use the second form on the Query Domains page.
• Given two domains, or one domain and a linear motif, use the Query Interaction page to check whether there is a direct interaction, or use the Path Query to find all pathes of minimal length between your domains.

Motif-based

• To retrieve information on a specific linear motif, use the Motif Query. You can give the exact name of the motif, or use the wildcard character %. If no exact match is found, 3did will return a list of similar motif names. The results for direct matches will include Motif Information for each motif in 3DID that matches your input.
• Given a motif and its binding domain, use the Query Interaction page to chech whether there is a direct interaction. You can also use the Path Query to find all pathes of minimal length between your motif and domain.

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.

Sequence-based

• Paste your sequence in fasta format on the Query Domains page. Blast will find all the PfamA domains, which will appear in the graphical view of your sequence, linked to the 3DID information on each domain.
• Given a PDB code at the PDB query page, 3DID produces a graph visualizing all the chains and domains in this PDB with their interactons. Chains with the same domains are clustered. In addition, there is a detailed view of each chain, showing domains and their positions, interactions referencing this protein, and GO terms it has been annotated with.

GO-based

• 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 domain name	SH3_1
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	HMM profile interface residues in SH3_1 binding partner(s) SH3_1 , P53 , p47_phox_C , SAMP , LIG_SH3_3 (...[PV]..P, from ELM)
A link to the Pfam entry	Pfam: PF00018.19
A menu with GO terms for this domain, if any	GO:0007596 - blood coagulation (biological_process) GO:0016021 - integral to membrane (cellular_component)
A menu with PDB chains containing this domain	1a0n, Chain B (2-58) 1abo, Chain A (1-56) 1abo, Chain B (1-56) 1abq, Chain A (1-55) 1ad5, Chain A (3-58) 1ad5, Chain B (3-58) 1aey, Chain A (3-57) ...
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 see below).

Domain-Domain Interaction View

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 1 0 : 2
PDB examples of this domain-domain interaction	PDB ID chain 1 residues chain 2 residues score Z-score Topology more information Visualization 1w98 B 229-355 A 4-286 8.29 3.86663 2 : 2 1w98 2cci B 309-431 C 4-286 3.34 2.32536 2 : 0 2cci
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 involved. 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 code.
SimInts	pkinase pkinase interaction Fold d.144 d.144 Plot Superfamily d.144.1 d.144.1 Plot Family d.144.1.2 d.144.1.2 Plot
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.
Experimental Information	Method Protein 1 domain Protein 2 domain cip YBR160W 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

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.	PDB ID domain chain residues motif chain residues motif sequence context residues topology more information visualization 1gh6 B 645-766 A 103-107 LFCSE 13 0 1gh6 1gux B 645-766 E 2-6 LYCYE 3 0 1gux

Interface Visualization

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 this domain. 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.

Path view

PDB view

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.

Sequence view

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) legend: : Clat_adaptor_s (1-142)  : LIG_Clathr_ClatBox_1 (78-82)

Graph View

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.