CL.46

BETA-SECRETASE 1

PDB

The ligand-free form

1sgz_B [Alignment: 1]

The ligand-bound form

2f3e_C[Alignment: 1]

View

Animations of

the structural change


Using Jmol

Function

EC*1

CSA distance*2

3.4.23.46

2.6

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

Ligand

PDB*1

Full name

AXQ

{(E)-(3R,6S,9R)-3-[(1S,3R)-3-((S)-1 -BUTYLCARBAMOYL-2-ETHYL-PROPYLCARB AMOYL)-1-HYDROXY-BUTYL]-6-METHYL-5, 8DIOXO-1,11-DITHIA-4,7-DIAZA-CYCLO PENTADEC-13-EN-9-YL}CARBAMIC ACID TERT-BUTYL ESTER

*1 Ligand name designated by the PDB identifiers.

Segments

Component No.

Fixed*1

Moving*1

Motion type

Ligand binding

Coupled motion type

1

D1(46C-48C,1C-68C,75C-157C,171C-290C,296C-359C,368C-374C,382C-385C)

L2(158C-170C)

Local

Independent

2

D1

L3(69C-74C)

Local

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

Yes

-7

2

3.3

*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

2

0.91

*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

Free

Independent

2

*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.

Link ::.