CL.27

PENICILLIN-BINDING PROTEIN 2X

PDB

The ligand-free form

1qme_A [Alignment: 1]

The ligand-bound form

1pyy_A[Alignment: 1]

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Animations of

the structural change


Using Jmol

Function

EC*1

CSA distance*2

8.7

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

Ligand

PDB*1

Full name

OSU

N-OCTANOYLSUCROSE

*1 Ligand name designated by the PDB identifiers.

Segments

Component No.

Fixed*1

Moving*1

Motion type

Ligand binding

Coupled motion type

1

D1(73A-91A,183A-204A,211A-231A,257A-373A,385A-615A,632A-750A)

L2(120A-141A,149A-164A)

Local

Independent

2

D1

L3(616A-631A)

Local

Independent

3

D1

L4(374A-384A)

Local

Coupled

Closure

4

D1

L5(92A-98A)

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

Yes

+38

2

Yes

+11

3

4.5

4

Yes

+6

*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

3

0.35

4

*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

Independent

3

4

*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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