ID.15

REGULATOR OF NONSENSE TRANSCRIPTS 1

PDB

The ligand-free form

2gk7_A [Alignment: 1]

The ligand-bound form

2gk6_A[Alignment: 1]

View

Animations of

the structural change



Using Jmol

Function

EC*1

CSA distance*2

3.6.1.-

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

Ligand

PDB*1

Full name

ADP

ADENOSINE-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(297A-336A,339A-348A,356A-366A,374A-400A,406A-582A,588A-660A,667A-700A,722A-724A,818A-820A)

D2(661A-666A,701A-721A,725A-817A,821A-843A,850A-906A)

Domain

Independent

2

D1

L3(347A-355A)

Local

Independent

3

D1

L4(582A-582A,587A-592A)

Local

Independent

4

D1

L5(367A-373A)

Local

Independent

5

D1

L6(384A-390A)

Local

Independent

6

D1

L7(401A-407A)

Local

Independent

7

D2

L8(844A-849A)

Local

Independent

8

D2

L9(902A-906A)

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

2.5

2

Yes

-7

3

3.5

4

Yes

+7

5

4.6

+1

6

Yes

+5

7

Yes

-6

8

5.7

*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.

Crystal environment

Component No.

Open state*1

Crystal packing*2

1

Bound

Coupled

2

3

Free

Independent

4

5

Free

Coupled

6

7

8

Bound

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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