CL.41

GANGLIOSIDE GM2 ACTIVATOR

PDB

The ligand-free form

1pu5_A [Alignment: 1]

The ligand-bound form

2ag4_B[Alignment: 1]

View

Animations of

the structural change


Using Jmol

Ligand

PDB*1

Full name

LP3,OLA

(7R)-4,7-DIHYDROXY-N,N,N-TRIMETHYL-10-OXO-3,5,9-TRIOXA4-PHOSPHAHEPTACOSAN-1-AMINIUM 4-OXIDE,OLEIC ACID

*1 Ligand name designated by the PDB identifiers.

Segments

Component No.

Fixed*1

Moving*1

Motion type

Ligand binding

Coupled motion type

1

D1(1B-87B,94B-129B,135B-164B)

L2(88B-93B)

Local

Coupled

Opening

2

D1

L3(130B-134B)

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

3.8

2

6.9

-3

*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

0.8

2

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

Crystal environment

Component No.

Open state*1

Crystal packing*2

1

2

Free

Coupled

*1 Distinction between the open state and the closed state required for examining the influence of the crystal environment.
*2 Crystal packing: Whether the change in the crystal environment is coupled with the structural change.

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