ATP binding domain 4 Structures

General information

General information from PDB indicates that :

(a) 1RU8 is a putative n-type ATP pyrophosphatase isolated from Pyrococcus furiosus, expressed in Escherichia Coli.

(b) Is a member of clan PP-loop

(c) Resolution of 2.7 angstroms, with an r-value of 0.218.

(d) Ligand chemical component identified as TRS (2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL).

Surface Structure

Pymol Visualization

Figure 1. The three-dimensional structure of secondary structure 1RU8, as generated by PyMOL

Purple- Helix
Yellow - Sheet
Green- Loop

Figure 2. The three-dimensional surface structure of 1RU8, as generated by PyMOL

Note that there is a artificial ligand (purple) bound to the protein

1RU8 is a dimer

Figure 3. 1RU8 indicates its a dimer

Secondary Structure and Location of PP-loop

Figure 4. Conserved residues of 1RU8

Potential Ligand Binding Interaction

Electrostatic Surface Potential

Figure 5. The electrostatic surface potential. Blue colour indicated positive charge and red colour indicated negative charge surface whereas white colour indicated neutral charge

Structure Similarities

Figure 6. The list of structural similarities to 1RU8 obtained using DALI. Highlighted by the box is the most similar structure that has known function which are used in this investigation.

Z score , the statistical significance of the similarity between protein-of-interest and other neighbourhood proteins. The program optimizes a weighted sum of similarities of intramolecular distances.

Root Mean Square Distance (RMSD), root-mean-square deviation of C-alpha atoms in the least-squares superimposition of the structurally equivalent C-alpha atoms. RMSD is not optimized and is only reported for information.

lali, the number of structurally equivalent residues.

nres, or the total number of amino acids in the hit protein.

%id, percentage of identical amino acids over structurally equivalent residues.

Structure Alignment

1RU8 and 2NZ2

Figure 7. Structure alignment between 1RU8 and 2NZ2

1RU8 and 3BL5

Figure 8. Structure alignment between 1RU8 and 3BL5

Surface Clefts

Figure 9. Surface clefts of 1RU8 generated via PDBsum

Surface Topography

Figure 10. The topology of 1RU8 generated via CASTp