Table 1. Complex structures and binding affinities of ubiquitin-binding domains.

The K_d values are for mono-ubiquitin unless otherwise specified. Protein data bank identification codes (PDB ID) (http://www.rcsb.org) are only listed for co-ordinates containing ubiquitin-binding domains complexed with ubiquitin unless otherwise specified. ITC, isothermal titration calorimetry; SPR, surface plasmon resonance; Ub, ubiquitin.

		Binding affinity		Structure
Ub-binding domain	Source protein	Kd (μM)	Method	PDB ID	Method (resolution, Å)	Note	Reference
UBA	Dsk2	14.8±5.3	SPR	1WR1	NMR		[47]
	hHR23A	400±100 (mono-Ub)	NMR	1ZO6	NMR	UBA2–two Ub	[48]
	Mud1	390±50 (mono-Ub)	SPR	1Z96	X-ray (1.8)	PDB for UBA alone	[55]
	Ede1	83±9	NMR	2G3Q	NMR		[49]
CUE	Vps9	20±1	ITC	1P3Q	X-ray (1.7)	Dimeric CUE	[52]
	Cue2	155±9	NMR	1OTR	NMR	Monomeric CUE	[53]
GAT	GGA3	181±39	ITC	1YD8	X-ray (2.8)	Two Ub-binding sites; Ub binds to site 1 in the crystal structure	[72]
	GGA3			1WR6	X-ray (2.6)		[73]
	TOM1	409±13	SPR	1WRD	X-ray (1.75)		[74]
UEV	Vps23			1UZX	X-ray (1.85)		[88]
	Tsg101	510±35	SPR	1S1Q	X-ray (2.0)		[87,89]
Ubc	UbcH5	∼300	NMR	2FUH	NMR		[90]
UIM	Vps27	277±8 (UIM1)	NMR	1Q0W	NMR	UIM1–Ub	[27]
		177±17 (UIM2)
	Vps27	246±1 (UIM1)	SPR	1O06	X-ray (1.45)	UIM2 only; no Ub	[26]
		1690±40 (UIM2)
	S5a	∼350 (UIM1)	NMR	1YX5	NMR		[29]
	S5a	73 (UIM2)	NMR	1YX6	NMR		[28,29]
DUIM	Hrs	190 (wt)	SPR	2D3G	X-ray	Two Ub-binding sites	[32]
	491 (site 1)
	543 (site 2)
MIU	Rabex-5	29±4.8 (Y25A, SPR)	SPR, ITC	2FID, 2FIF	X-ray (2.5)		[30]
		29±1 (Y26A, ITC)
		28.7	ITC	2C7N	X-ray (2.1)		[31]
NZF	Npl4	126±26	SPR	1Q5W	NMR		[79]
A20 ZnF	Rabex-5	22±0.4 (A58D, SPR)	SPR, ITC	2FID, 2FIF	X-ray (2.5)		[30]
		21±1 (A58D, ITC)
	Rabex-5	12	ITC	2C7N	X-ray (2.1)		[31]
ZnF UBP	Isopeptidase T	2.8	ITC	2G45	X-ray (2.0)		[82]