CL.25

COPROPORPHYRINOGEN III OXIDASE

PDB

The ligand-free form

2qt8_AB [Alignment: 1 2]

The ligand-bound form

3dwr_AB[Alignment: 1 2]

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the structural change



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Function

EC*1

CSA distance*2

1.3.3.3

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

Ligand

PDB*1

Full name

6x0PA

6x(cyclopentylacetic 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(3A-29A,35A-36A,44A-65A,90A-112A,125A-301A,1B-38B,44B-65B,89B-114B,122B-299B)

L3(66B-88B)

Local

Coupled

Closure

2

D1

L4(115B-121B)

Local

Independent

3

D1

L5(39B-43B)

Local

Independent

4

D2(66A-68A,84A-89A,113A-124A)

L6(69A-83A)

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

-16

2

Yes

-5

3

Yes

-5

4

Yes

-15

*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

0.58

2

3

4

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

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