Table 1.

PDZ domains used for MD simulations.

Protein	PDZ	Class	PDB code	Residue Ids	Ligand Length	Ligand Sequencea
NHERF	PDZ1	Apo	1G9O93	A:10−94
		I	1GQ518	A:10−94/A:95−99	5	-EDSFL (`a' pep.)
		I	1GQ418	A:10−94/A:95−99	5	-NDSLL (`b' pep.)
		I	1I9233	A:10−94/A:95−99	5	-QDTRL (`c' pep.)
PSD-95	PDZ3	Apo	1BFE3	A:306−415
		I	1BE93	A:306−415/B:5−9	5	-KQTSV
Dishevelle d		Apo	1L6O32	A:254−340
		I	1L6O32	A:254−340/D:1−8	8	-SLKLMTTV
Shankb		Apo	1Q3O34	A:584−686
		I	1Q3P34	A:584−686/C:1−6	6	-EAQTRL
Syntenin	PDZ2	Apo	1NTE21	A:197−270
		I	1OBX21	A:197−270/B:5−8	4	-(ETLE)DSVF
		II	1OBY21	B:197−270/Q:1−6	6	-TNEFYA
Erbin		Apo	1MFG20	A:1280−1367
		I	1N7T30	model 2 A:12−99/B:301−307	7	-TGWETWV
		II	1MFG20	A:1280−1367/B:1247−1255	9	-EYLGLDVPV
GRIP	PDZ6	Apo	1N7E94	A:668−753
		II	1N7F94	A:668−753/B:1−8	8	-ATVRTYSC
Inad	PDZ1	Apo	1IHJ.31	A:12−105
		II	1IHJ.31	A:12−105/D:3−7	5	-(GK)TEFCA

^aResidues in parenthesis are disordered in the crystal structure and were not included in the MD simulations.

^bThe coordinates of residues 602 to 621 in the holo structure were taken from the crystal structure of the apo form of Shank (PDB code: 1Q3O), see “Molecular Systems” subsection in Materials and Methods.