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Table 4 Comparison of the disulfide bond configurations in proteins that have very similar X-ray and NMR structures.

From: Search for allosteric disulfide bonds in NMR structures

Protein

X-Ray

NMR

Structural Similarity

 

PDB

resolution

disulfides

configuration

DSE, kJ.mol -1

PDB

models

disulfides

configuration 1

DSE, kJ.mol -1

RMSD 3

MaxSub 4

thioredoxin

2tir

2

32–35

+/-RHHook

 

1xoa

20

32–35

-RHHook (15)

 

0.93

0.93

         

+/-RHHook (5)

   

ferredoxin II

1fxd

1.7

18–42

+/-RHSpiral

 

1f2g

15

18–42

-RHHook (5)

 

0.96

0.93

         

+/-LHStaple (5)

   
         

+/-RHSpiral (5)

   

ribonulcease A

1kf5

1.1

26–84

-LHSpiral

7.1

2aas

32

26–84

-LHSpiral (16)

12.6 (11.8–13.3)2

1.1

0.92

         

-RHHook (13)

   
         

-RHSpiral (3)

   
   

40–95

-LHSpiral

4.3

  

40–95

-LHSpiral (32)

4.1 (3.4–4.8)

  
   

58–110

-LHSpiral

10.7

  

58–110

-LHSpiral (30)

11.4 (11.1–11.7)

  
         

-RHHook (2)

   
   

65–72

-LHHook

   

65–72

-RHHook (32)

   

ovomucoid

2ovo

1.5

8–38

-LHSpiral

6.1

1tur

12

8–38

-LHSpiral (12)

23.0 (20.6–25.4)

2.04

0.89

   

16–35

+/-LHSpiral

   

16–35

-LHSpiral (11)

   
         

-RHSpiral (1)

   
   

24–56

-RHHook

6.4

  

24–56

-RHHook (6)

11.1 (10.4–11.8)

  
         

-LHHook (3)

   
         

-LHStaple (3)

   

tendamistat

1hoe

2

11–27

-/+RHHook

 

2ait

9

11–27

+/-LHStaple (9)

 

3.57

0.87

   

45–73

-LHSpiral

   

45–73

-RHHook (3)

   
         

-RHSpiral (2)

   
         

-LHSpiral (1)

   
         

+/-LHStaple (1)

   
         

+/-RHHook (1)

   
         

-LHHook (1)

   

erabutoxin B

3ebx

1.4

3–24

-LHSpiral

2.8

1fra

14

3–24

-LHSpiral (11)

23.2 (13.7–32.7)

1.42

0.87

         

-LHHook (2)

   
         

-RHHook (1)

   
   

17–41

-LHSpiral

   

17–41

-RHHook (11)

   
         

-LHHook (1)

   
         

-/+LHHook (1)

   
         

+/-RHHook

   
   

43–54

-RHSpiral

   

43–54

-LHSpiral (6)

   
         

-RHSpiral (5)

   
         

-RHHook (2)

   
         

-RHStaple (1)

   
   

55–60

+RHSpiral

10.4

  

55–60

+RHSpiral (9)

38.1 (35.5–40.6)

  
         

+/-RHSpiral (4)

   
         

+LHSpiral (1)

   

lipid transfer protein

1mzl

1.9

4–52

-LHSpiral

 

1afh

15

4–52

+/-RHSpiral (10)

 

1.67

0.84

         

-RHHook (3)

   
         

-RHSpiral (2)

   
   

14–29

+/-RHHook

   

14–29

+/-LHStaple (5)

   
         

+/-RHHook (3)

   
         

-LHStaple (3)

   
         

-/+LHHook (2)

   
         

-LHHook (2)

   
   

30–75

-LHSpiral

4.4

  

30–75

-LHSpiral (12)

23.9 (22.4–25.3)

  
         

-LHHook (2)

   
         

-RHHook (1)

   
   

50–89

+/-LHSpiral

   

50–89

+/-LHHook (6)

   
         

-LHSpiral (5)

   
         

+/-LHSpiral (3)

   
         

+/-RHHook (1)

   

β-lactoglobulin

1bsy

2.2

66–160

-RHSpiral

9.3

1dv9

21

66–160

-RHSpiral (4)

39.9 (29.5–50.3)

2.36

0.83

         

-LHSpiral (3)

   
         

+/-LHSpiral (3)

   
         

-/+LHHook (3)

   
         

+/-RHStaple (2)

   
         

-LHHook (2)

   
         

+/-RHSpiral (1)

   
         

+/-RHHook (1)

   
         

+/-LHStaple (1)

   
         

-/+RHHook (1)

   
   

106–119

-RHStaple

15.8

  

106–119

-RHStaple (12)

18.6 (17.1–20.2)

  
         

-LHStaple (8)

   
         

-LHHook (1)

   

ribonulcease T1

4rnt

2.2

2–10

-LHHook

15.3

1ygw

34

2–10

-LHHook (16)

26.6 (26.5–26.8)

1.82

0.82

         

+/-RHStaple (10)

   
         

-/+RHHook (4)

   
         

-RHStaple (3)

   
         

-RHHook (1)

   
   

6–103

-RHStaple

11.7

  

6–103

-RHStaple (28)

28.9 (25.8–32.1)

  
         

-RHHook (6)

   

β2-microglobulin

1lds

1.8

25–80

-LHStaple

 

1jnj

20

25–80

-LHSpiral (10)

 

3.46

0.77

         

-RHSpiral (7)

   
         

-RHHook (3)

   
  1. 1 Numbers in brackets are the number of disulfides with that configuration.
  2. 2 The mean dihedral strain energy (DSE) and 95% confidence intervals.
  3. 3 The root-mean square deviations (RMSD) value was calculated between all Cα atoms of the X-ray structure and the first NMR model [16].
  4. 4 MaxSub is a measure of structural similarity of the X-ray and NMR structures [16]. A score of 1.0 means that all Cα atoms are matched between the X-ray and NMR structures, while a score towards zero indicates very different structures. All the structures listed in the table have only small-scale differences (MaxSub values from 0.77 to 0.93).