ID.2

LYSYL-TRNA SYNTHETASE

PDB

The ligand-free form

1bbw_AA [Alignment: 1 2]

The ligand-bound form

1bbu_AA[Alignment: 1 2]

View

Animations of

the structural change


Using Jmol

Function

EC*1

CSA distance*2

6.1.1.6

2.2

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

Ligand

PDB*1

Full name

2xLYS

2x(LYSINE)

*1 Ligand name designated by the PDB identifiers.

Segments

Component No.

Fixed*1

Moving*1

Motion type

Ligand binding

Coupled motion type

1

D1(17A-153A,161A-190A,210A-214A,218A-234A,236A-240A,257A-268A,270A-277A,301A-302A,311A-314A,479A-479A,481A-500A,200A-209A,235A-235A,240A-256A,278A-300A,303A-310A,314A-326A,382A-388A,413A-443A,456A-478A,480A-480A)

D2(200A-209A,235A-235A,241A-256A,278A-300A,303A-310A,315A-326A,382A-388A,414A-443A,456A-478A,480A-480A,17A-153A,161A-190A,210A-214A,218A-234A,236A-239A,257A-268A,270A-277A,301A-302A,311A-313A,479A-479A,481A-500A)

Domain

Independent

2

D1

D3(327A-381A,389A-412A)

Domain

Independent

3

D1

L4(444A-455A)

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

1

3

Yes

+12

*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

Free

Coupled

3

*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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