analysing conserved water molecules of thrombin structures

~/combine2go/data/thrombin/pdb/water/thrombin.water.percent-sort.pdb

thrombin_water.png

In the figure thrombin model 3 (white), the superimposed ligands (blue) and conserved water molecules (spheres) with an occurence of more than 50 % among the 40 compared structures. The color of the water molecules is according to their occurance (blue 50 % - red 100 %).


55 berlagerte Strukturen:
../align/
1a4w.pdbf 1bmm.pdbf 1c4v.pdbf 1d6w.pdbf 1g32.pdbf 1gj5.pdbf 1mu6.pdbf 1o0d.pdbf 1sl3.pdbf 8kme.pdbf
1ae8.pdbf 1bmn.pdbf 1c4y.pdbf 1d9i.pdbf 1ghv.pdbf 1jwt.pdbf 1mu8.pdbf 1o2g.pdbf 1ta2.pdbf
1afe.pdbf 1c1u.pdbf 1c5n.pdbf 1dwc.pdbf 1ghw.pdbf 1k21.pdbf 1mue.pdbf 1o5g.pdbf 1ta6.pdbf
1aix.pdbf 1c1v.pdbf 1d3d.pdbf 1dwd.pdbf 1ghx.pdbf 1k22.pdbf 1nm6.pdbf 1oyt.pdbf 1tom.pdbf
1bcu.pdbf 1c1w.pdbf 1d3p.pdbf 1ets.pdbf 1ghy.pdbf 1kts.pdbf 1nt1.pdbf 1qbv.pdbf 1uma.pdbf
1bhx.pdbf 1c4u.pdbf 1d3q.pdbf 1fpc.pdbf 1gj4.pdbf 1ktt.pdbf 1nzq.pdbf 1sb1.pdbf 7kme.pdbf

~/Program/WatCH/WatCH/bin/prep_WatCH 55 ../align/8kme.pdbf thrombin.water

analyse_water.sh -f thrombin.water -n 55

FATAL ERROR: more than MAX_NUMBER_OF_INPUT_POINTS points (read_input_file)

nur die ersten 40 Strukturen:
analyse_water.sh -f thrombin.water.tmp -n 40

sort -k 9 -r thrombin.water.tmp.percent.pdb thrombin.water.percent-sort.pdb

Ergebnisse
wichtige Wasser in der active site:
permanent:
HETATM O HOH 29 5.408 -1.048 29.745 1.00 90.00
HETATM O HOH 6 7.717 -5.288 24.048 1.00102.50
HETATM O HOH 19 -0.001 -1.657 26.568 1.00102.50

on/off wichtig:
HETATM O HOH 14 8.007 -1.381 21.666 1.00 75.00
HETATM O HOH 87 5.700 -1.174 27.350 1.00 50.00

on/off weniger wichtig ab in der active site:
HETATM O HOH 23 1.447 12.107 19.747 1.00 72.50
HETATM O HOH 195 8.513 5.186 27.960 1.00 35.00
HETATM O HOH 37 13.476 5.797 22.259 1.00 47.50
HETATM O HOH 224 15.281 10.599 18.328 1.00 30.00
HETATM O HOH 187 12.255 8.689 20.887 1.00 22.50

on/off weniger wichtig am Rande der active site:
HETATM O HOH 81 -3.600 4.122 27.918 1.00 65.00

------------------------------------------------------------------
ATOM 4665 O WAT 401 5.408 -1.048 29.745 1.00 90.00
ATOM 4666 O WAT 402 7.717 -5.288 24.048 1.00102.50
ATOM 4667 O WAT 403 -0.001 -1.657 26.568 1.00102.50
ATOM 4668 O WAT 404 8.007 -1.381 21.666 1.00 75.00
ATOM 4669 O WAT 405 5.700 -1.174 27.350 1.00 50.00
ATOM 4670 O WAT 406 1.447 12.107 19.747 1.00 72.50
ATOM 4671 O WAT 407 8.513 5.186 27.960 1.00 35.00
ATOM 4672 O WAT 408 13.476 5.797 22.259 1.00 47.50
ATOM 4673 O WAT 409 15.281 10.599 18.328 1.00 30.00
ATOM 4674 O WAT 410 12.255 8.689 20.887 1.00 22.50
ATOM 4675 O WAT 411 -3.600 4.122 27.918 1.00 65.00

folgende Wasser wieder rausgenommen:
406 - 411
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