Table I.

Structurally Known, Covalently Linked Complexes

N-terminus protein/peptide	Linker	C-terminus protein/peptide	PDB	Method	Reference
Unstable proteins and their interacting partners:
a. MHC Class II molecules and peptide complexes:
HSP70 peptide	GGGGSLVPRGSGGGGS	MHC Class II I-Ek	1IEB	X-ray	31
Influenza virus hemagglutinin peptide	GSGSGS	MHC Class II I-Ad	1IAO	X-ray	32
Ovalbumin peptide	GSGSGS	MHC Class II I-Ad	2IAD	X-ray	32
Hen egg lysozyme	GGGGSLVPRGSGGGGS	MHC Class II I-Ak	1IAK	X-ray	33
Hen egg lysozyme	GGGGSLVPRGSGGGGS	MHC Class II I-Ag7	1F3J	X-ray	34
pHB (64–76 of the d allele of mouse β globin)	GGGGSLVPRGSGGGGS	MHC Class II mut IEk (E11Q, D66N on α chain)	1I3R	X-ray	35
Mylein Basic Protein (1-11)	eight residues of GS	MHC Class II I-Au	1K2D	X-ray	36
Pigeon Cytochrome c	GGGGSLVPRGSGGGGS	MHC Class II I-Ek	1KTD	X-ray	37
Moth Cytochrome c	GGGGSLVPRGSGGGGS	MHC Class II I-Ek	1KT2	X-ray	37
Eα 3K peptide	GGGGSLVPRGSGGGGS	MHC Class II I-Ab	1LNU	X-ray	38
class II invariant chain-associated peptide (CLIP)	GSGSGS	MHC Class II I-Ab	1MUJ	X-ray	39
hypocretin	GGGGSLVPRGSGGGG	MHC class II DQ0602	1UVQ	X-ray	40
Mylein Basic Protein (124-135)	GSGSGS	MHC Class II I-Au	2P24	X-ray	41
Tu elongation factor	GGGGSLVPRGSGGGGS	DR52c	3C5J	X-ray	42
HLA-DR α-chain	GGGGSLVPRGSGGGGS	HLA-DP2	3LQZ	X-ray	43
Gliadin	GGGGSLVPRGSGGGGS	HLA-DQ2.3	4D8P	X-ray	44
b. LIM binding and related proteins:
LIM only protein, LMO2	GGSGGHMGSGG	LIM domain-binding protein 1(Ldb1)	—	NMR	45
LIM only protein, LMO4, LMO2	GGSGGHMGSGG	LIM domain-binding protein 1(Ldb1)	1M3V, 1J2O	NMR	29
LIM only protein, LMO4	GGSGGSGGSGG	LIM domain-binding protein 1(Ldb1)	1RUT	X-ray	23
LIM only protein, LMO4	GGSGGSGGSGG	LIM domain-binding protein 1(Ldb1)	2DFY	X-ray	46
LIM homeobox protein 3, Lhx3	GGSGGHMGSGG	Isl1 (Islet-1)	2RGT	X-ray	47
LIM domain-binding protein 1(Ldb1)	GGSGGHMGSGG	LIM homeobox protein 3, Lhx3	2JTN	NMR	48
LIM only protein, LMO2-LIM2	GGSGGSGGSGG	LIM domain-binding protein 1(Ldb1)	—	NMR	48
LIM only protein, LMO2	GGSGGSGGSGG	LIM domain-binding protein 1(Ldb1)	2L6Y, 2L6Z	NMR	49
LIM homeobox protein 4, Lhx4	GGSGGHMGSGG	Isl2 (Islet-2)	3MMK	X-ray	30
LIM only protein, LMO4	GGSGGHMGSGG	CtlP (C-terminal binding protein interacting protein)	—	NMR	50
c. PXR-ligand binding domain and SRC-1:
PXR-LBD	GGSGG	SRC-1	3CTB, 3CTC, 3HVL	X-ray	51
Transient protein–protein interactions:
a. TCR-peptide-MHC molecule complexes:
1. Peptide bound to MHC molecule:
hen egg CA peptide (residues 134 to 146)	GGGGSLVPRGSGGGGS	MHC Class II I-Ak	1D9K	X-ray	52
Eα 3K peptide	GGGGSLVPRGSGGGGS	MHC Class II I-Ab	3C6L, 3C5Z, 3C60	X-ray	53
Mylein Basic Protein (114-126)	GGGGSLVPRGSGGGGS	HLA-DR4	3O6F	X-ray	54
2. Peptide bound to TCR:
Hemagglutinin HA peptide	GGSGGGGG	TCR HA 1.7	1FYT	X-ray	55
Hemagglutinin HA1	GGSGGGGG	TCR HA1.7	1J8H	X-ray	56
Mylein Basic Protein (89-101)	GGSGGGGG	TCR 3A6	1ZGL	X-ray	57
Mylein Basic Protein (85-99)	GGSGGGGG	TCR Hy.1B11	3PL6	X-ray	58
b. Others:
Phosphoprotein (457–507) of paramyxoviral polymerase from measeles virus	GSGSGSGS	Nucleocapsid protein (486–505) of measeles virus	1T6O	X-ray NMR	14
FtsY	31 amino acids glycine-serine rich linker	Ffh	2XKV	Cryo-EM	59
Minor coat gene 3 protein (g3p)	GGGSEGGGSEGGGSE GGG	Integral membrane protein TolA (coreceptor)	1TOL	X-ray	6
Asf1 (anti-silencing function 1)	AAGAATAA	Histone H3	2IDC	X-ray	60
CaM	GGGGG	CBD of calcineurin	2F2P, 2F2O	X-ray	61
Covalently linked dimers:
a. HIV-1 PR:
HIV-1 protease	GGSSG	HIV-1 protease	1HPX	X-ray	62
C95M HIV-1 protease	GGSSG	HIV-1 protease	1G6L	X-ray	63
C95M HIV-1 protease	GGSSG	C1095A HIV-1 protease	1LV1	X-ray	64
HIV-1 protease	GGSSG	HIV-1 protease	2NPH	X-ray	65
HIV-1 protease	GGSSG	HIV-1 protease	3DOX	X-ray	66
HIV-1 protease	GGSSG	HIV-1 protease	2WHH	X-ray	67
G48V/C95F HIV-1 protease	GGSSG	G48V/C95F HIV-1 protease	3N3I	X-ray	68
HIV-1 protease	GGSSG	HIV-1 protease	3MIM	X-ray	69
HIV-1 protease	GGSSG	HIV-1 protease	4EP2, 4EPJ, 4EP3, 4EQJ, 4EQ0	X-ray	70
b. TTR dimer:
Transthyretin	GSGGGTGGGSG	Transthyretin	1QWH	X-ray	71
GluR S1-S2 complex:
GluR0 S1	GT	GluR0 S2	1II5, 1IIT, 1IIW	X-ray	72
GluR2 S1	GT	GluR2 S2	1FTK, 1FTL, 1FTO, 1FW0, 1FTJ, 1FTM	X-ray	73
GluR5/6 S1	GT	GluR5/6 S2	1S9T, 1SD3, 1S50, 1S7Y	X-ray	74
Recently determined structures:
Fat domain of focal adhesion kinase	GSGSGSGSGGSG GSGGSGGSGGSGGS	Ld4 motif of paxillin	2L6H	NMR	—
Fat domain of focal adhesion kinase	GSGGSGSGGSGGSG	Ld2 motif of paxillin	2L6G	NMR	—
Fat domain of focal adhesion kinase linked to Ld2 motif of paxillin at its C-terminus via GSGGSGSGGSGGSG linker	GSGSGSGSGGSG GSGGSGGSGGSGGS	Ld4 motif of paxillin	2L6F	NMR	—