ATP binding domain 4 Structures: Difference between revisions
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Note that there is a artificial ligand, TRS (purple) bound to the protein]] | Note that there is a artificial ligand, TRS (purple) bound to the protein]] | ||
[[Image:1RU8 as 2 domain.png|right|thumb|500px|'''Figure 2.1'''. 1RU8 indicates its a dimer]] | [[Image:1RU8 as 2 domain.png|right|thumb|500px|'''Figure 2.1'''. 1RU8 indicates its a dimer]] | ||
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== Secondary Structure and Location of PP-loop == | == Secondary Structure and Location of PP-loop == | ||
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[[Image:1RU8 conserved residues.PNG|left|thumb|500px|'''Figure 4'''. Conserved residues of 1RU8 via PDBsum]] | [[Image:1RU8 conserved residues.PNG|left|thumb|500px|'''Figure 4'''. Conserved residues of 1RU8 via PDBsum]] | ||
[[Image:1RU8-conserved region n interact with ligand.png|right|thumb|500px|'''Figure 5'''. Conserved residues of 1RU8 based on figure 4 visualized in Pymol. Highlighted red is the really conserved region and highlighted blue is the residues that is conserved and interact with the ligand ]] | [[Image:1RU8-conserved region n interact with ligand.png|right|thumb|500px|'''Figure 5'''. Conserved residues of 1RU8 based on figure 4 visualized in Pymol. Highlighted red is the really conserved region and highlighted blue is the residues that is conserved and interact with the ligand ]] | ||
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== Electrostatic Surface Potential == | == Electrostatic Surface Potential == |
Revision as of 12:42, 2 June 2009
General Properties
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
Secondary Structure and Location of PP-loop
Electrostatic Surface Potential
Structure Similarities
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
Highlighted in green is the 2NZ2 while in magenta is the 1RU8. Since 1RU8 has 2 domain, domain B is coloured darker in magenta for differentiation. There are 2 ligand indicated by the yellow (Citrulline) and red (ATP) spheres from 2NZ2. Highlighted also is the conserved region of PP-loop in pink and blue for 1RU8 and 2NZ2 respectively.
1RU8 and 3BL5