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Table 1 Properties of known binding sites of the dataset proteins.

From: Relating destabilizing regions to known functional sites in proteins

Pdb ida Holo-pdb idsb N resc F resd ASAe F ASAf Cleftg
Small       
1e1a   13 4.2 272 2.1 T
1e3f 1bm7, 1e4h, 1e5a, 1eta, 1tha 8 6.9 193 1.0 T
1gu7 1guf, 1n9g 31 8.5 1158 3.7 T
1gud 1rpj 24 8.3 976 7.4 T
1gus 1gug, 1gun, 1guo 4 6.0 119 0.9 F
1gush 1gug, 1gun, 1guo 14 20.9 110 0.8 F
1gxy 1og1, 1og3, 1og4 24 10.8 947 8.7 T
1hf8 1hfa, 1hg2, 1hg5 4 1.5 329 1.4 F
1hhq 1hiy, 1b4s, 1b99, 1bux 17 11.3 1006 2.8 T
1is5 1is3, 1is4, 1is6 22 16.4 663 3.0 T
1jcf 1jcg 34 10.1 820 5.6 F
1odl 1odi, 1odj 25 10.7 339 0.8 T
1ofn 1oi6 15 7.4 669 4.0 T
1tm2 1tjy 19 6.1 437 3.2 T
1upq 1upr 12 11.2 783 11.9 T
1usg 1usk, 1usi 15 4.3 268 1.0 T
1usl 2bes, 2bet 18 11.5 505 3.9 T
1w1h 1w1d, 1w1g 10 6.6 560 6.2 T
1w2i 1w2i 8 8.9 450 5.0 F
1w37 1w3i, 1w3n, 1w3t 12 4.1 107 0.3 T
1y2t 1y2x, 1y2w 27 19.0 1191 5.6 F
Polysaccharide       
1nof   12 3.1 471 3.2 T
1o88   15 4.2 472 3.5 T
1ob0 1e3z 41 8.5 1572 8.9 T
1ogb 1e6n, 1e6r, 1h0g, 1h0i, 1ogg 16 3.2 565 1.5 T
1qhz 1qi2, 8a3h, 4a3h, 1e5j, 1qi0 14 4.6 590 5.2 T
1qjv   10 2.9 265 1.8 T
1uuq 1uz4 16 3.9 256 1.7 T
1w0n 1ux7 8 6.7 642 11.2 T
1w6z 1sf7, 1sfb, 1sfg 20 15.5 891 13.6 T
1w9s 1w9t, 1w9w 12 9.0 376 5.9 F
Peptide       
1c7k   9 6.8 275 4.2 T
1e5t 1e8m, 1e8n, 1o6g, 1qfs, 1uop 18 2.5 485 1.7 T
1ea7   7 2.3 97 0.9 T
1gt9 1gtj, 1gtl 21 5.9 450 3.4 F
1kl4 1hqq, 1kl3, 1kl5, 1rsu 17 14.2 854 4.2 T
1oes 1g1f, 1g1g, 1g1h, 1ptt, 1ptu 16 5.7 885 6.6 T
1r29 1r2b 29 23.8 1760 13.8 F
Protein       
1e3f 1qab, 1rlb 15 13.0 971 5.0 F
1e6l 1bdj 10 7.9 775 11.7 F
1e6l 1a0o, 1eay, 1ffg, 1ffs, 1ffw 15 11.8 1212 18.4 T
1eao 1e50, 1h9d 26 22.8 1819 28.2 F
1f2x   12 9.5 604 5.2 F
1gcp 1gcq 21 31.3 1405 33.2 F
1gqv 2bex 36 26.7 2246 28.9 F
1obq 1gka 22 12.2 1023 6.1 T
1sif 1cmx, 1fxt, 1nbf, 1otr, 1q5w, 1s1q, 1uzx 14 19.7 937 21.7 T
1tgr 1h59 15 28.8 1236 29.5 T
1uns 1jck 19 8.1 1620 13.5 F
1uns 1jwm 20 8.5 1386 11.6 F
1uol 1gzh, 1kzy 18 9.2 1301 13.1 F
1uq4 2aai 42 16.0 2796 21.6 F
1w53   12 14.3 770 8.8 T
Nucleic acid       
1e7l   8 5.1 352 2.0 T
1eao 1h9d, 1hjb 18 15.8 1375 21.3 F
1gqv 1hi3, 1hi4, 1hi5 9 6.7 245 3.2 T
1gv2 1h88, 1h89, 1mse 30 29.1 2289 30.2 T
1o7i   5 4.3 497 7.4 F
1okb 1emh, 1emj, 1q3f, 1ssp, 2ssp, 4skn 30 13.5 1539 15.0 T
1uol 1tsr, 1tup 19 9.7 1229 12.4 F
1uq4 1apg, 1br5 17 6.5 364 2.8 T
1utx   10 15.2 691 9.0 F
1vyi   10 9.0 1009 15.0 F
Lipid       
1obq 1h91, 1i4u, 1s2p, 1s44 21 11.6 350 2.1 T
1qmd   14 3.8 465 2.9 F
Metal       
1e6l 1chn, 1ymv 7 5.5 350 5.3 T
1qmd 1kho 6 1.6 67 0.4 T
Peptide-Protein       
1mix 1mk7, 1mk9 26 12.6 1526 11.9 F
Small-Metal       
1h1y   19 8.6 365 2.2 T
1h6l 2poo, 1h6l 16 4.5 627 4.4 T
1oid 1ho5, 1hp1, 1hpu 19 3.6 872 3.9 F
Polysaccharide-Metal       
1gkb 1bxh, 1cjp, 1c57, 1ces, 1dq1, 1gkb, 3cna, 3enr 19 8.0 586 1.8 F
Lipid-Metal       
1umv 1pob, 1umv, 1c1j 17 13.9 492 3.8 T
Protein-Metal       
1o6v 1o6s 49 10.6 2224 11.3 F
  1. Properties of known binding sites of the dataset proteins. Binding sites are classified according to their type of ligand. The last 5 categories refer to binding sites where 2 types of ligand can bind.
  2. aPdb identifier of structure used for energy calculations.
  3. bPdb identifiers of the structures of the protein-ligand complex used to define the binding site.
  4. cNumber of residues in binding site.
  5. dFraction of protein residues in binding site (in %).
  6. eTotal ASA of binding site residues.
  7. fFraction of protein ASA in binding site (in %).
  8. gTrue (T) if binding site sits in a cleft, False (F) otherwise.
  9. h1gus appears twice here because it has 2 distinct binding sites for small ligands. The same observation applies to 1e6l and 1uns that have 2 distinct binding sites for different proteins.