Table 4.

3D-structures of USPs available in the PDB and searched with DALI server against the Model_USP-691-A.

PDB-chain-domain	Z-score	RMSD	lalia	nresb	% id	Protein (domain number)	Organism	Cofactor	ATP binding motif		References
3s3t-A	26.2	0.4	143	145	31	Putative USP	Lactobacillus plantarum	ATP	Typical	G-2X-G-9X-GS	n/a
3ab8-A-d1	19.2	1.7	137	144	33	TTHA0350 (d1)	Thermus thermophilus	ATP	Similar	G-2X-G-10X-GS	Iino et al., 2011
3hgm-B	18.8	2.5	138	147	33	TEAD	Halomonas elongata	ATP	Typical	G-2X-G-9X-GS	Schweikhard et al., 2010
1mjh-A	18.7	2.0	139	143	31	MJ0577	Methanococcus jannaschii	ATP	Typical	G-2X-G-9X-GS	Zarembinski et al., 1998
3cis-C-d1	18.0	1.9	137	148	23	Rv2623 (d1)	Mycobacterium tuberculosis	ATP	Typical	G-2X-G-9X-GS	Drumm et al., 2009
3cis-C-d2	17.5	2.6	136	140	22	Rv2623 (d2)	M. tuberculosis	ATP	Typical	G-2X-G-9X-GS	Drumm et al., 2009
2z09-A	16.9	1.6	120	124	33	USP family	T. thermophilus	ACP	Typical	G-2X-G-9X-GS	n/a
2z08-A	16.8	1.7	119	123	34	USP family	T. thermophilus	ATP	Typical	G-2X-G-9X-GS	n/a
4wny-A	16.5	1.9	127	132	28	USP	Burkholderia pseudomallei	none	–		n/a
1wjg-A	16.4	1.8	124	135	30	Probable ATP binding	T. thermophilus	none	Typical	G-2X-G-9X-GS	n/a
2z3v-A	16.2	2.1	126	137	29	USP family	T. thermophilus	none	Typical	G-2X-G-9X-GS	n/a
5ahw-B	16.2	2.2	121	127	29	USP MSMEG_3811	M. smegmatis	cAMP/ATP	Typical	G-2X-G-9X-GS	Banerjee et al., 2015
3olq-A-d1	15.8	3.0	136	146	17	USP E (d1)	Proteus mirabilis	none	–		n/a
4r2l-A	15.7	2.8	135	142	25	YnaF	Salmonella enterica	ATP	–		Bangera et al., 2015
3fg9-E	15.5	2.5	135	150	26	UspA family	Lb. plantarum	none	–		n/a
3qtb-B	15.5	2.5	126	133	26	AF0826	Archaeoglobus fulgidus	dAMP	–		Tkaczuk et al., 2013
3dlo-C	15.4	2.2	124	133	26	AF0826	A. fulgidus	none	–		Tkaczuk et al., 2013
4r2m-A	15.3	2.8	133	141	25	YnaF	S. enterica	ANP	–		Bangera et al., 2015
3fh0-B	15.3	2.7	124	125	27	Putative USP KPN_01444	Kleibsiella pneumonia	ADP	–		n/a
3fdx-A	15.0	2.6	123	127	27	USP F	K. pneumonia	ATP	–		n/a
–	–
3ab8-A-d2	13.8	2.1	111	115	24	TTHA0350 (d2)	T. thermophilus	ATP	Degenerated	G-8X-GS	Iino et al., 2011
3olq-A-d2	12.8	3.4	131	159	14	USP E (d2)	P. mirabilis	none	–		n/a

^aMatching residues.

^bTotal number of residues.