Table 1. Dataset of 32 protein–RNA complexes selected from the NDB (December 7, 1999).

	Family	PDB	NDB	Protein name	Protein recognition	RNA type	RNA structure	Res.
A	1	1A34	PRV020	Coat protein STMV	β-sheet	vRNA	Double-stranded	1.81
	2	1BMV	PRV001	Coat protein BPMV	β-sheet	vRNA	Single-stranded	3.00
	3	2BBV	PRV004	Coat protein BBV	Groove binding	vRNA	Double-stranded	2.80
	4	1ZDI	PRV006	Coat protein, Bacteriophage MS2	β-sheet	vRNA	Single-stranded, single loop	2.70
		1ZDH	PRV003	Coat protein, Bacteriophage MS2	β-sheet	vRNA	Single-stranded, single loop	2.70
		1ZDJ	PRV021	Coat protein, Bacteriophage MS2	β-sheet	vRNA	Single-stranded, single loop	2.70
		1ZDK	PR0003	Coat protein, Bacteriophage MS2	β-sheet	vRNA	Single-stranded, single loop	2.86
		1AQ3	PRV008	Coat protein, Bacteriophage MS2	β-sheet	vRNA	Single-stranded, single loop	2.80
		1AQ4	PRV009	Coat protein, Bacteriophage MS2	β-sheet	vRNA	Single-stranded, single loop	3.00
		5MSF	PR0001	Coat protein, Bacteriophage MS2	β-sheet	vRNA	Single-stranded, single loop	2.80
		6MSF	PRV010	Coat protein, Bacteriophage MS2	β-sheet	vRNA	Single-stranded, single loop	2.80
		7MSF	PR0002	Coat protein, Bacteriophage MS2	β-sheet	vRNA	Single-stranded, single loop	2.80
	5	1A1T	N/A	Nucleocapsid protein HIV-1	Groove binding	vRNA	Single-stranded, single loop	NMR
B	6	1ASY	PTR005	Aspartyl-tRNA synthetase	Groove binding + β-sheet	Asp-tRNA	Single-stranded, multiple loops	3.00
		1ASZ	PTR008	Aspartyl-tRNA synthetase (+ATP)	Groove binding + β-sheet	Asp-tRNA	Single-stranded, multiple loops	3.00
	7	1QTQ	PTE003	Glutaminyl-tRNA synthetase	Groove binding + β-sheet	Gln-tRNA	Single-stranded, multiple loops	2.40
		1GTS	PTR002	Glutaminyl-tRNA synthetase (+AMP)	Groove binding + β-sheet	Gln-tRNA	Single-stranded, multiple loops	2.80
		1GSG	PTR001	Glutaminyl-tRNA synthetase (+ATP)	Groove binding + β-sheet	Gln-tRNA	Single-stranded, multiple loops	2.80
		1GTR	PTR003	Glutaminyl-tRNA synthetase (+ATP)	Groove binding + β-sheet	Gln-tRNA	Single-stranded, multiple loops	2.50
		1QRS	PTR009	Glutaminyl-tRNA synthetase	Groove binding + β-sheet	Gln-tRNA	Single-stranded, multiple loops	2.60
		1QRT	PTR010	Glutaminyl-tRNA synthetase	Groove binding + β-sheet	Gln-tRNA	Single-stranded, multiple loops	2.70
		1QRU	PTR011	Glutaminyl-tRNA synthetase	Groove binding + β-sheet	Gln-tRNA	Single-stranded, multiple loops	3.00
	8	1SER	PTR004	Seryl-tRNA synthetase	Groove binding	Ser-tRNA	Single-stranded, multiple loops	2.90
	9	1QF6	N/A	Threonyl-tRNA synthetase	Groove binding + β-sheet	Thr-tRNA	Single-stranded, multiple loops	2.90
	10	1TTT	PTR012	Elongation factor Tu	Groove binding + β-sheet	Phe-tRNA	Single-stranded, multiple loops	2.70
		1B23	PDR0004	Elongation factor Tu	Groove binding + β-sheet	Cys-tRNA	Single-stranded, multiple loops	2.60
	11	1QA6	N/A	L11	Groove binding	23S rRNA	Single-stranded, multiple loops	2.60
C	12	1AV6	PRV007	Methyltransferase VP39	Groove binding	MRNA	Single-stranded	2.70
	13	1A9N	PTR016	Spliceosomal U2B″/U2A′ complex	β-sheet	snRNA	Single-stranded, single loop	2.38
		1URN	PRV002	U1A spliceosomal protein	β-sheet	snRNA	Single-stranded, single loop	1.92
		1AUD	N/A	U1A spiceosomal protein	β-sheet	snRNA	Single-stranded, multiple loops	NMR
	14	1B7F	N/A	Sex-lethal protein	β-sheet	mRNA	Single-stranded	2.60

The structures have been divided into those that bind viral RNA (A), those involved in protein synthesis (B) and those involved in RNA modification (C). STMV, Satellite tobacco mosaic virus; BPMV, bean pod mosaic virus; BBV, black beetle virus.

The PDB codes shown in bold are those structures included in the non-homologous dataset used for the interface parameter calculations (see Materials and Methods).