CD.8

SUCROSE HYDROLASE

PDB

The ligand-free form

3cze_A [Alignment: 1]

The ligand-bound form

3czk_A[Alignment: 1]

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the structural change



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An image of the result of

the linear response theory


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Function

EC*1

CSA distance*2

3.2.1.48

2.1

*1 Enzyme commission number.
*2 The distance between the active site annotated in CSA23 and the ligand-binding sites.

Ligand

PDB*1

Full name

SUC

SUCROSE

*1 Ligand name designated by the PDB identifiers.

Segments

Component No.

Fixed*1

Moving*1

Motion type

Ligand binding

Coupled motion type

1

D1(81A-128A,145A-146A,149A-172A,320A-321A,323A-332A,334A-342A,346A-435A,442A-607A,624A-635A)

D2(8A-19A,24A-80A,129A-144A,147A-148A,173A-221A,228A-319A,333A-333A,343A-345A)

Domain

Coupled

Closure

2

D1

L3(608A-608A,620A-623A)

Local

Independent

3

D2

L4(222A-228A)

Local

Coupled

Closure

4

D2

L5(18A-23A)

Local

Independent

*1 The location of the fixed and moving segments indicated by the residue number assigned in the ligand-bound form. The background color of characters indicates the corresponding segment in the structure. The colored segments not described in the Table are: 1) a part of component in which the motion is small (< 1.0 A), or, 2) a part of a protomer of homodimers, for which a corresponding part of the other protomer is shown in the Table.

Displacement and disorder

Component No.

RMSD*1

Displacement*2

Disorder-order transition*3

Disorder residue*4

Helix-Coil*5

1

1.2

2

Yes

+5

3

Yes

+6

4

Yes

+4

*1 The root-mean-square displacement of a component of motion calculated for the domain motions.
*2 The mean displacement of a component of motion calculated for the local motions.
*3 Order-disorder transition: Whether the open form contains the disordered structure.
*4 The number of disordered residues.
*5 The number of residues exhibiting the alpha-helix to coil transition.

Linear response

Component No.

Correlation coefficient*1

1

0.93

2

3

4

*1 The correlation coefficient between the displacement vector predicted by the linear response theory and the one observed in the crystal structures.

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