ID.5

TETRACYCLINE REPRESSOR PROTEIN

PDB

The ligand-free form

2ns7_AB [Alignment: 1 2]

The ligand-bound form

2ns8_CD[Alignment: 1 2]

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Animations of

the structural change



Using Jmol

Ligand

PDB*1

Full name

PEPT(WTWNAYAFAAPS),PEPT(WTWNAYAFAAP)

Peptide(WTWNAYAFAAPS),Peptide(WTWNAYAFAAP)

*1 Ligand name designated by the PDB identifiers.

Segments

Component No.

Fixed*1

Moving*1

Motion type

Ligand binding

Coupled motion type

1

D1(65C-86C,114C-130C,140C-142C,185C-206C,47D-92D,95D-155D,164D-201D)

D2(7C-64C,87C-104C,133C-139C,143C-155C,162C-184C)

Domain

Independent

2

D1

L3(154D-160D,164D-165D)

Local

Coupled

Closure

3

D2

L4(156C-161C)

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

1.8

2

Yes

+5

3

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.

Crystal environment

Component No.

Open state*1

Crystal packing*2

1

Free

Coupled

2

3

*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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