PDBnet Bird's eye view of network in structurome

PDBnet Help

Glossary of terms used in PDBnet

These are some of the commonly used terms in the PDBnet website.

PDB Code or PDBID

Protein Data Bank entry code for the protein. Enter the four letter PDB-Code that has to be queried. Protein chain information is not necessary. ( Query Example : 1a5k or 1A5K )

Molecule

Name of the molecule about the chain. ( Molecule Example : UREASE for PDB=1a5kA )

Genus

Genus name of the molecule. This is written in PDB as Scientific Name. ( Genus Example : KLEBSIELLA AEROGENES for PDB=1a5kA )

Length

The number of the amino acid residues in the protein.

Chain Type

Type of chain. Choose the type of chain which is protein or nucleic acid. ( Chain Type Example : A,B and C for PDB=1a5k)

Molecule Type

Type of PDB molecule. Choose the type from protein, nucleic acid, protein-nucleic acid or carbohydrate.

Representative molecule for each cluster

Name of molecule with the highest appearance in the cluster.

Cluster List

List of clusters of the protein chains. The items of the list are network ID and Complex Cluster included in each cluster, etc.

Cluster List with links to nucleic acids

List of clusters of the protein chains that interact with nucleic acid chains. The items of the list are network ID and Complex Cluster included in each cluster as well as Cluster List.

Cluster ID

ID for the cluster. Uniprot ID(uniref90 or uniref50).

Chains in this cluster

Number of chians that belong to the cluster.

Clusters links

Number of links for the clusters.

Cluster ID search

Enter the Five columns of number Cluster ID that has to be queried. ( Query Example : P17693 )

Network ID

ID of network to which the cluster belongs. Network ID is beginning at LN0000.

Network ID search

Enter the four columns of number Network ID next to "LN" that has to be queried. ( Query Example : LN0123 )

Avg length

Average length of chains included in the cluster.

Max length

Maximum length of chains included in the cluster.

Min length

Minimum length of chains included in the cluster.

Nucleic acid chain

Nucleic acid chain PDB ID that belongs to this network.

Network List

List of networks between clusters of the protein chains.

Network List containing nucleic acids

List of networks containing nucleic acids.

Cluster in this network

Number of clusters in the network.

top cluster

One cluster of clusters in network.

Edge: interaction link

Number of cluster edge(link) in this network.

hard link

Physical interaction, with distance between atoms from difference chains less than 5 angstrom..

soft link

Indirect interaction link.

Cluster-Nucleic acid PDB chain link

Interaction link between protein cluster and nucleic acid PDB chain. These interaction from complex PDB chains contain proteins and nucleci acids.

CATH

Hierarchical classification database of protein domain structures.

Pfam

Database of multiple sequence alignments and hidden Markov models covering many common protein domains and families.

E.C.No.

Enzyme Commission number.

Number of chains with link

Number of chains that are linked.

PDB-chain

PDBID(4letters) and chainID(1letter).

Top rank chain

The longest chain in this cluster.

Chain-ID

Chain ID code for the protein molecule or nucleic acid molecule in PDB-ID.

Header

Name of molecule in the PDB entry.

Title

The title of the experiment or analysis that is represented in the PDB entry.

Synonym

Another name.

Fragment

Describes a subset of residues from the whole gene product that was used for determining the structure.

Type

Type of molecule such as protein or nucleic acids.

Physical Contact

This table shows the interactions among the chains involved in the complex structure. The protein-protein interactions (p-p) are displayed in yellow, protein-nucleic acid interactions (p-n) in cyan, and nucleic acid-nucleic acid interactions (n-n) in green. "Details" shows a list of all the atom-atom pairs between the query chain and the other chains within a threshold distance of 5 angstrom.

Chains with Homology

Number of chains that have homology .

Chime display

Three dimension of structure display by Chime.

Jmol display

Three dimension of structure display by Jmol.

PDB entry

Display of PDB entry file.

Information at PDB

An information portal to biological macromolecular structures.

3DinSight

3DinSight ( an integrated database and search tool for structure, property and function of biomolecules ) entry

Protein-Nucleic Acid Complex Database

Database of protein-nucleic acid complex.

e-value

A parameter that describes the number of hits one can "expect" to see just by chance when searching a database of a particular size.