IL.34

DNA TOPOISOMERASE I

PDB

The ligand-free form

1mw9_X [Alignment: 1]

The ligand-bound form

1cy0_A[Alignment: 1]

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the structural change



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Function

EC*1

CSA distance*2

5.99.1.2

29.9

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

Ligand

PDB*1

Full name

A3P

ADENOSINE-3'-5'-DIPHOSPHATE

*1 Ligand name designated by the PDB identifiers.

Segments

Component No.

Fixed*1

Moving*1

Motion type

Ligand binding

Coupled motion type

1

D1(12A-24A,138A-151A,195A-213A,272A-356A,365A-403A,429A-434A,473A-545A)

L3(357A-364A)

Local

Independent

2

D2(223A-248A,257A-271A,404A-428A,435A-438A,449A-464A)

L4(439A-441A,446A-448A)

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

+8

2

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.

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