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Table 1 List of protein-RNA complexes used in the present study

From: Structure based approach for understanding organism specific recognition of protein-RNA complexes

Complex

Organism

PDB code

RMSD (Å)

Sequence identity (%)

Binding site residues

Protein (%)

RNA (%)

Elongation Factor TU

E. coli

1OB2:A

1.4

71

7.63

22.37

T. aquaticus

1OB5:A

9.14

20.78

Leucyl-tRNA synthetase

E. coli

4ARC:A

1-2: 1.9

1-2: 45

4.09

25.29

T. thermophilus

2BTE:A

1–3: 2.5

1–3: 27

3.08

22.89

P. horikoshii

1WZ2:A

2–3: 1.6

2–3: 29

3.21

18.18

Retinoic acid inducible protein I

A. platyrhynchos

4A36:A

2.6

59

4.14

28.95

H. sapiens

3TMI:A

  

3.17

42.86

Glutamyl-tRNA synthetase

T. maritima

3AKZ:A

2.3

41

9.65

33.78

T. thermophilus

1N78:A

  

9.19

30.67

Aspartyl-tRNA synthetase

E. coli

1IL2:A

1-2: 2.1

1-2: 49

7.12

32.00

T. thermophilus

1EFW:A

1–3: 2.2

1–3: 28

3.97

20.55

S. cerevisiae

1ASY:A

2–3: 2.3

2–3: 30

8.57

26.67

Signal recognition particle

H. sapiens

1MFQ:C

1-2: 2.7

1-2: 36

9.30

6.25

M. jannaschii

2V3C:C

1–3: 5.4

1–3: 32

5.79

18.48

S. solfataricus

1QZW:A

2–3: 1.29

2–3: 48

2.50

11.70

ATP dependent RNA helicase

H. sapiens

3G0H:A

1.1

51

5.19

100.00

S. cerevisiae

3PEY:A

  

5.57

83.33

Tyrosyl-tRNA synthetase

S. cerevisiae

2DLC:X

1-2: 1.7

1-2: 35

2.79

5.26

M. jannaschii

1J1U:A

1–3: 2.7

1–3: 26

4.58

6.49

T. thermophilus

1H3E:A

2–3: 2.2

2–3: 27

4.63

16.28

Probable exosome complex exonuclease 1

A. fulgidus

3M7N:D

0.9

59

2.33

33.33

P. abyssi

2PO1:A

  

3.21

40.00

50S ribosomal protein L7Ae

A. fulgidus

1RLG:A

0.8

60

13.45

36.00

M. jannaschii

1SDS:A

  

17.09

23.33

60S ribosomal protein L7

S. cerevisiae

3O5H:G

1.9

47

1.23

1.65

T. thermophila

4A1C:V

  

2.51

5.00

STAR family quaking protein

C. elegans

4JVY:A

2.8

58

10.20

71.43

H. sapiens

4JVH:A

  

8.61

63.64

Retinoic acid inducible protein I

A. platyrhynchos

4A2X:A

1.7

55

3.05

14.29

H. sapiens

3NCU:A

  

7.46

25.00

Arginyl-tRNA synthetase

S. cerevisiae

1F7U:A

2.6

29

7.25

32.89

P. horikoshii

2ZUF:A

  

6.20

32.05

Pumilio mRNA binding factor

S. cerevisiae

3 K49:A

1.1

45

9.49

90.00

H. sapiens

2YJY:A

  

7.43

90.00

tRNA pseudouridine synthase B

E. coli

1K8W:A

1.8

34

11.31

54.55

T. maritime

1R3E:A

  

10.36

70.59

Signal recognition particle 19 kDa protein

M. jannaschii

1LNG:A

2.1

34

35.82

16.49

S. solfataricus

3KTW:A

  

22.94

19.79

Phenylalanyl-tRNA synthetase

T. thermophiles

2IY5:A

2.1

31

3.14

7.89

H. sapiens

3TUP:A

  

4.58

25.00

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Biology Direct

ISSN: 1745-6150

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