CD.41

SUGAR ABC TRANSPORTER, PERIPLASMIC SUGAR-BINDING PROTEIN

PDB

The ligand-free form

3c6q_B [Alignment: 1]

The ligand-bound form

3c6q_D[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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Ligand

PDB*1

Full name

XYP

BETA-D-XYLOPYRANOSE

*1 Ligand name designated by the PDB identifiers.

Segments

Component No.

Fixed*1

Moving*1

Motion type

Ligand binding

Coupled motion type

1

D1(104D-235D,282D-303D)

D2(3D-103D,236D-281D)

Domain

Coupled

Closure

*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

4.2

*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

0.95

*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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