ID.3

HISTIDYL-TRNA SYNTHETASE

PDB

The ligand-free form

1h4v_BB [Alignment: 1 2]

The ligand-bound form

1ady_AB[Alignment: 1 2]

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Animations of

the structural change


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Function

EC*1

CSA distance*2

6.1.1.21

0.5

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

Ligand

PDB*1

Full name

2xHAM

2x(HISTIDYL-ADENOSINE MONOPHOSPHATE)

*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-56A,63A-116A,121A-273A,280A-421A,2B-56B,63B-116B,121B-166B,170B-171B,229B-264B,266B-273B,280B-419B)

D2(167B-169B,172B-228B,265B-265B)

Domain

Independent

2

D1

L3(52A-62A)

Local

Independent

3

D1

L4(52B-62B)

Local

Independent

4

D1

L5(274A-279A)

Local

Independent

5

D1

L6(274B-279B)

Local

Independent

6

D1

L7(116A-120A)

Local

Coupled

Closure

7

D1

L8(116B-120B)

Local

Coupled

Closure

8

D1

L9(259B-263B)

Local

Coupled

Closure

*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

2.2

2

Yes

+6

+7

3

Yes

+6

+7

4

Yes

+6

5

Yes

+6

6

Yes

+4

7

Yes

+4

8

5.5

*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

2

3

4

5

6

7

8

0.96

*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

Bound

Coupled

2

Free

Coupled

3

Free

Independent

4

5

6

7

8

*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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