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Table 1 Features of proteins with substantial structural change in non-interacting regions and no/moderate change at interface

From: Comparison of tertiary structures of proteins in protein-protein complexes with unbound forms suggests prevalence of allostery in signalling proteins

 

PDB code

Cα RMSD

Normalized PB substitution score

Protein

Bound

Unbound

IR*

NIR_PBc*

Difference

IR*

NIR_PBc*

Difference

     

(NIR_PBc – IR)

  

(NIR_PBc – IR)

PIP3 kinase (O)

1HE8_r

1E8Z

0.49

8.45

7.96

1.25

-1

-2.25

HISF protein (O)

1GPW_r

1THF

0.68

8.10

7.42

1.68

-1.31

-2.99

UCH-L3 (O)

1XD3_r

1UCH

1.30

5.11

3.80

1.35

-1.05

-2.4

Son of Sevenless (O)

1BKD_r

2II0

1.33

4.91

3.57

1.39

-0.82

-2.21

TGF-beta (O)

1KTZ_r

1TGK

0.66

4.41

3.75

2.1

-0.95

-3.05

HPr kinase C-ter domain (E)

1KKL_r

1JB1

1.76

4.00

2.24

1.95

-0.98

-2.93

Cystatin (E)

1YVB_l

1CEW

0.63

3.85

3.21

2.43

-1.24

-3.67

DH/PH domain of TRIO (O)

2NZ8_r

1NTY

1.33

3.77

2.43

1.25

-0.78

-2.03

Actin (O)

2BTF_r

1IJJ

1.08

3.77

2.68

1.76

-0.81

-2.57

Alpha-1-antitrypsin (E)

1OPH_r

1Q1P

0.92

3.50

2.58

1.35

-1.39

-2.74

TGFbeta receptor (O)

1B6C_l

1IAS

1.17

3.14

1.96

1.28

-1.04

-2.32

Vitamin D binding protein (O)

1KXP_l

1KW2

1.53

3.11

1.57

1.66

-0.77

-2.43

TolB (O)

2HQS_r

1CRZ

1.37

3.04

1.67

2

-0.81

-2.81

RCC1 (O)

1I2M_l

1A12

0.40

3.00

2.60

2.43

-0.99

-3.42

Sporulation response factor B (O)

1F51_r

1IXM

0.78

2.70

1.92

1.1

-0.97

-2.07

Ran GTPase (O)

1A2K_l

1QG4

0.33

2.57

2.24

2.56

-1.03

-3.59

HEW lysozyme (A)

1BVK_l

3LZT

0.31

2.57

2.25

2.86

-1.06

-3.92

Transferrin receptor ectodomain (O)

1DE4_l

1CX8

0.94

2.51

1.57

1.04

-1.16

-2.2

Anthrax toxin receptor (O)

1T6B_l

1SHU

0.27

2.32

2.05

2.15

-0.75

-2.9

Xylanase inhibitor (E)

2B42_r

1T6E

0.33

2.25

1.91

2.06

-0.95

-3.01

Fab (A)

1E6J_r

1E6O

0.75

1.98

1.22

2.48

-0.73

-3.21

Complement C3 (O)

1GHQ_r

1C3D

0.21

1.58

1.36

1.92

-0.69

-2.61

  1. *The abbreviations used are: IR - Interface regions, NIR_PBc – Non-interacting regions with PB change, l – ligand (smaller of the two proteins in the complex), r – receptor (bigger of the two proteins in the complex), E – enzyme-inhibitor complex, A – Antigen-antibody complex, O – Other complexes.
  2. The proteins are listed in decreasing order of average Cα RMSD of NIR_PBc values. The average Cα RMSD of IR and NIR_PBc is 0.89 and 3.75, respectively. The normalized PB substitution score for IR and NIR_PBc values is 1.78 and -0.98, respectively.