CL.3

PROTEIN-ARGININE DEIMINASE TYPE IV

PDB

The ligand-free form

1wd8_AA [Alignment: 1 2]

The ligand-bound form

1wd9_AA[Alignment: 1 2]

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the structural change


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Function

EC*1

CSA distance*2

3.5.3.15

7.5

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

Ligand

PDB*1

Full name

8xCA

8x(CALCIUM ION)

*1 Ligand name designated by the PDB identifiers.

Segments

Component No.

Fixed*1

Moving*1

Motion type

Ligand binding

Coupled motion type

1

D1(4A-33A,39A-53A,68A-97A,100A-124A,136A-154A,177A-217A,225A-312A,317A-322A,320A-330A,351A-369A,389A-395A,403A-515A,523A-632A,645A-663A,4A-33A,39A-53A,68A-97A,100A-124A,136A-154A,177A-217A,225A-308A,320A-330A,351A-369A,389A-395A,403A-515A,523A-632A,645A-663A)

L2(155A-176A)

Local

Coupled

Closure

2

D1

L3(370A-388A)

Local

Coupled

Closure

3

D1

L4(633A-644A)

Local

Independent

4

D1

L5(309A-312A,317A-319A)

Local

Independent

5

D1

L6(396A-402A)

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

+14

2

Yes

+17

3

Yes

+12

4

Yes

+3

5

Yes

+7

*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

0.83

2

3

4

5

*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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