Relating destabilizing regions to known functional sites in proteins

Dessailly, Benoît H; Lensink, Marc F; Wodak, Shoshana J

doi:10.1186/1471-2105-8-141

BMC Bioinformatics

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

From: Relating destabilizing regions to known functional sites in proteins

Pdb id^a	Holo-pdb ids^b	N res^c	F res^d	ASA^e	F ASA^f	Cleft^g
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
1gus^h	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

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.
^aPdb identifier of structure used for energy calculations.
^bPdb identifiers of the structures of the protein-ligand complex used to define the binding site.
^cNumber of residues in binding site.
^dFraction of protein residues in binding site (in %).
^eTotal ASA of binding site residues.
^fFraction of protein ASA in binding site (in %).
^gTrue (T) if binding site sits in a cleft, False (F) otherwise.
^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.

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ISSN: 1471-2105

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