Sandbox3H04

This is a default text for your page Sandbox3H04. Click above on edit this page to modify. Be careful with the < and > signs.

You may include any references to papers as in: the use of JSmol in Proteopedia ^[1] or to the article describing Jmol ^[2] to the rescue.

General Structure and Origins

The total structure weighs 31.41 kDa and the atom count is 2,297. The protein 3H04 usually only occurs in bacteria, specifically staphylococcus aureus subsp. aureus Mu50. Each chain in the protein is about 275 residues long. Using InterPro, it can be seen that the protein is found in the alpha-beta hydrolase superfamily.

Family and Superfamily

Structure/Sequence Analysis

Sequence Analysis

SPRITE

The first structural analysis completed was SPRITE to search the structure of 3H04 for configurations of amino acid side chains with similar structure to known enzyme active sites. Resulting hits occurred with 1a8q Bromoperoxidase A1 with an RMSD of 0.13 that had three amino acid matches. A second match, 1pfp, had an RMSD of 0.15 and three different amino acid matches within the functional group. The overlapped image can be found here [1] to view structure similarity. A third match, 1n8o, was viewed with an RMSD of 1.01 and four different amino acid matches within the functional group for better alignment with the overlap shown here [2].

Chimera

The structural viewing program Chimera was used to view the specific amino acids from SPRITE in the theorized functional group. 1a8q was the primary match used to model matching H304’s 104 serine at 1a8q’s 94, 220 aspartate at 223, and 248 histidine at 252 respectively with a RMSD of 0.452. An overlap was performed to view the functional alignment which can be viewed here [].

Structure Analysis

DALI

DALI was used to overlay an entire protein and look at similarity between both proteins. A high Z-score is desired to show the quality of alignment to the query and a high %id as a report of sequence identity between the structures. The first match was 2qruA with a Z-value of 32.5 and 27% id however the protein is also uncharacterized which does not assist in a proposed function. The second match 8q03-B had a Z-value of 25.9 and an %id of 19%. The section originates from ORF30 which had other high quality matches suggesting a pattern. ORF30 is short for Gene 30 protein which is researched and known as human herpesvirus 8 with an alpha/beta hydrolase fold-3 domain-containing pro. This suggests a function to our unknown 3H04 and a possible location where the protein can be found.

Proposed Functionality

Substrates and Docking Analysis

Hypothetical Function

Experimental Data

Relevance

Structural highlights

This is a sample scene created with SAT to by Group, and another to make of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.