Hi It looks to me as if there is a glitch in the sequence viewer for some PDB files like 4PFK. The symptom is that waters get mixed up among the protein sequences as in the snapshot here
http://pcwww.liv.ac.uk/~drigden/dross.png If you write the structure out again you get things like this ATOM 40 N GLY 5 20.601 -28.694 4.635 1.00 37.79 4PFK N ATOM 41 CA GLY 5 19.386 -28.380 5.423 1.00 41.21 4PFK C ATOM 42 C GLY 5 19.278 -26.841 5.426 1.00 42.59 4PFK C ATOM 43 O GLY 5 20.254 -26.164 5.038 1.00 43.67 4PFK O HETATM 44 O HOH 5 4.786 -19.354 8.074 1.00 34.51 4PFK O HETATM 45 O HOH 6 7.048 -4.823 8.185 1.00 20.29 4PFK O ATOM 46 N VAL 6 18.116 -26.349 5.824 1.00 38.63 4PFK N ATOM 47 CA VAL 6 17.842 -24.904 5.901 1.00 33.77 4PFK C ATOM 48 C VAL 6 16.826 -24.721 7.009 1.00 35.07 4PFK C ATOM 49 O VAL 6 15.935 -25.593 7.057 1.00 37.40 4PFK O ATOM 50 CB VAL 6 17.427 -24.327 4.537 1.00 31.75 4PFK C ATOM 51 CG1 VAL 6 16.199 -24.987 3.908 1.00 28.52 4PFK C ATOM 52 CG2 VAL 6 17.323 -22.819 4.592 1.00 25.99 4PFK C TER 53 VAL 6 HETATM 54 O HOH 7 7.246 -12.026 8.967 1.00 16.51 4PFK O ATOM 55 N LEU 7 16.985 -23.701 7.817 1.00 35.71 4PFK N ATOM 56 CA LEU 7 16.018 -23.467 8.906 1.00 38.35 4PFK C After playing a bit it seems as if it applies particularly to old, non-standard PDB files where a) Protein and HETATMs have the same chain ID (in the case of 4pfk, chain ID is blank for both) b) Water numbering overlaps protein residue numbering Wish I'd noticed this one yesterday too... Cheers Dan -- Dr Daniel John Rigden Tel:(+44) 151 795 4467 School of Biological Sciences FAX:(+44) 151 795 4414 Room 101, Biosciences Building University of Liverpool Crown St., Liverpool L69 7ZB, U.K.
