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Protein page

Each unique protein chain in the structure is described by a thumbnail image, wiring diagram and sequence and structural motifs, as described below.

a. Thumbnail image 
b. Motifs
c. Active site(s)
d. PROSITE pattern(s)
e. CATH domains
f. "Wiring diagram"
g. Topology diagrams
  Protein page

a. Thumbnail image

Where the protein chain is not the only molecule in the structure the thumbnail image(s), rendered using Raster3D, shows the protein chain's location in the structure by making all other molecules transparent. In the example on the left, therefore, the protein is shown as the solid purple object while the DNA, ligands and metals are all see-through.

Often the structure contains multiple copies of the same chain. In these cases, the representative chain is shown as solid while its copies are shown semi-transparent to distinguish them from any other molecules which are fully transparent.

Clicking on the image will show the chain alone.

The icons below the thumbnail display the chosen chain in the corresponding molecular graphics program. Both Jmol and Strap are Java applications, so only require that you have a java-enabled browser. RasMol, on the other hand, needs separate installation and browser configuration (see Using RasMol)

b. Motifs

The list of motifs shows the secondary structure motifs in the structre as computed by v.3.0 of Gail Hutchinson's PROMOTIF program.

The motifs are described in the PROMOTIF section of the documentation.

Also listed are any catalytic sites as defined in the Catalytic Site Atlas (CSA). Here only a single residue, Asp256 has been defined as catalytic and is highlighted on the wiring diagram.

c. Active site(s)

The active sites are as defined by the SITE records in the PDB file. Here there is a single site called ACT. Clicking on the link gives you a list of residues belonging to the site. The icon corresponds to the marker used on the wiring diagram to identify the site residues.

d. PROSITE pattern(s)

Where the protein sequence matches any PROSITE patterns, these are listed here. Clicking on the link shows the matching sequence. The colour coding of the sequence matches the colours of the bars under the corresponding amino acids in the wiring diagram. These colours are explained in the PROSITE section of the documentation.

e. CATH domains

The CATH domain definitions for the protein chain are listed here. The links go to the CATH database. The colours correspond to the colours of the amino acids in the wiring diagram below and the colouring of the sepatate topology diagrams.

f. Wiring diagram

The wiring diagram is a schematic diagram showing the protein's secondary structure elements (alpha-helices and beta-sheets) together with various structural motifs such as beta- and gamma-turns, and beta-hairpins. Helices are leballed H1, H2, etc while strands are labelled A, B, C, etc accoriding to the beta sheet to which they belong. If the protein contains any disulphide bonds, these are shown by yellow linking bars labelled with a numeric disulphide identifier.

The single-letter amino acid codes showing the protein's sequence are coloured according to their CATH structural domain. Catalytic residues are indicated by a box surrounding the amino acid code. Red dots above the single-letter codes signify residues that interact with any bound ligand(s), blue dots show interactions with DNA or RNA while green dots indicate metal binding residues. Coloured lines underneath the amino acid codes represent residues belonging to a PROSITE pattern, the redder the colour the more highly conserved the residue in the pattern.

Below the diagram is a key which summarised these annotations:

The magnifying glass on the right-hand side gives a high-resolution version of the diagram, expanded by a factor of 5, which is more suitable for inclusion in publications.

g. Topology diagrams

The topology diagrams show how the beta strands, represented by the large arrows, join up, side-by-side, to form beta-sheets and how the alpha-helices (the large cylinders) are located relative to these. The small arrows indicate the directionality of the protein chain, from the N- to the C-terminus. The numbers within the secondary structural elements correspond to the residue numbering given in the PDB file.

Clicking on one of the icons on the right gives a full-size version of the diagram in either PostScript or PDF format.

If, as here, the protein chain has been split into its constituent CATH domains, each domain has a separate diagram. Otherwise, a diagram of the whole chain is given.

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