Table 3.

Lys48-Glu51 distances for all DUB-ubiquitin complexes

UCH Family
PDB ID	DUB-ubiquitin complex	Lys48-Glu51 distance (Å)
1XD3	UCHL3-UbVME	9.1, 11.5*
1CMX	YUH1-Ubal	10.8
2WDT	PfUCHL3-UbVME	7.3, 9.6
3IFW	UCHL1 S18Y-UbVME	8.7
3KVF	UCHL1 I93M-UbVME	12.3
3KW5	UCHL1-UbVME	13.1
USP Family
PDB ID	DUB-ubiquitin complex	Lys48-Glu51 distance (Å)
3TMP	DUBA-Ubal	8.3
2Y5B	USP21-linear diUbal	7.8, 10.8, 6.6
1NBF	HAUSP-Ubal	10.0, 10.7
2AYO	USP14-Ubal	10.9
3MHS	SAGA complex (UBP8)-Ubal	9.2
2HD5	USP2, Ub	9.0
2G45	IsoT, Ub	8.6, 8.9
2J7Q	M48 USP-UbVME	9.9, 10.8
3V6E	USP2, Ub variant	7.0
3V6C	USP2, Ub variant	7.4
3IHP	USP5, Ub covalent	9.6, 6.3
3MTN	USP21, ubiquitin-based USP21-specific inhibitor	8.5
3IT3	USP21, Ub covalent	7.4, 7.5, 7.4, 7.4
3N3K	USP8, covalent Ub-like variant	10.4
3NHE	USP2a, Ub	7.4
2IBI	USP2, Ub covalent	7.6
OTU Family
PDB ID	DUB-ubiquitin complex	Lys48-Glu51 distance (Å)
4IUM	arterivirus papain-like protease 2, Ub	7.4
3ZNH	CCHF viral, Ub-propargyl	9.5
4I6L	OTUB1, Ub	9.1
3PT2	Viral OTU, Ub	10.7
4HXD	Nairovirus viral OTU, Ub	8.3, 10.1
3BY4	OTU, Ub	6.0
3PRM	CCHF viral OTU, Ub	9.5, 10.0
3PRP	CCHF viral OTU, Ub	10.3, 10.9
3C0R	OTU, Ub	8.4
4DHZ	h/ceOTUB1-ubiquitin aldehyde-UBC13∼Ub	9.2, 8.8
4DHJ	ceOTUB1 ubiquitin aldehyde UBC13∼Ub complex	11.4, 8.5, 6.9, 11.8, 9.8, 10.1
4DDI	OTUB1/UbcH5b∼Ub/Ub	7.5, 12.6, 12.6, 7.5, 12.6, 7.5
4DDG	OTUB1/UbcH5b∼Ub/Ub	11.3, 7.1, 8.0
3PHW	OTU Domain of CCHF Virus, Ub	7.6, 7.2, 9.0, 5.8
MJD Family
PDB ID	DUB-ubiquitin complex	Lys48-Glu51 distance (Å)
3O65	Ataxin-3-like, Ub	9.6, 11.4, 12.8, 11.5
2JRI	Ataxin 3, Ub	12.3, 12.9
JAMM Family
PDB ID	DUB-ubiquitin complex	Lys48-Glu51 distance (Å)
2ZNV	AMSH-LP, Lys63-linked diubiquitin	9.0, 8.3, 11.9, 11.3

^*Multiple distance entries refer to that in the other subunits of the crystallographic asymmetric unit.