ATP binding domain 4 Structures

Useful info

Here is some useful paper. check it out Link to Paper: http://pfam.sanger.ac.uk/family?acc=PF00764 Dali: http://ekhidna.biocenter.helsinki.fi/dali_server/results/20090512-0051-3897fbdf5431ad2e808e66dde1070610/index.html#alignment-7 Interpro: http://www.ebi.ac.uk/interpro/DisplayIproEntry?ac=IPR002761 (align 1RU8 & i. 11-16, 2NZ2 & i. 11-15)

SCOP Work: http://scop.mrc-lmb.cam.ac.uk/scop/data/scop.b.d.cj.c.b.bb.html

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

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

Purple- Helix
Yellow - Sheet
Green- Loop

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

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

Secondary Structure and Location of P-loop (ATP binding site)

1RU8 is a dimer

Electrostatic Surface Potential

Alignment of 1RU8 and 2NZ2

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.

1RU8 and 2NZ2

1RU8 and 3BL5

Surface Clefts

Surface Topography

Topology Diagram of 1RU8