CD.19

SUCCINYL-COA:3-KETOACID-COENZYME A TRANSFERASE 1

PDB

The ligand-free form

2nrb_AB [Alignment: 1 2]

The ligand-bound form

1o9l_AB[Alignment: 1 2]

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the structural change


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An image of the result of

the linear response theory


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Function

EC*1

CSA distance*2

2.8.3.5

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

Ligand

PDB*1

Full name

EMT

2-(ETHYLMERCURI-THIO)-BENZOIC 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(42A-66A,68A-121A,131A-166A,186A-286A,300A-519A,40B-66B,68B-286B,300B-400B,420B-440B,465B-517B)

D2(122A-130A,167A-185A)

Domain

Coupled

Opening

2

D1

L3(441B-464B)

Local

Independent

3

D1

L4(401B-419B)

Local

Independent

4

D1

L5(175B-180B)

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

1

2

Yes

-24

3

Yes

-19

4

3.6

*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

0.23

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.

Crystal environment

Component No.

Open state*1

Crystal packing*2

1

2

3

4

Free

Independent

*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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