CL.18

PYRROLYSYL-TRNA SYNTHETASE

PDB

The ligand-free form

2e3c_AA [Alignment: 1 2]

The ligand-bound form

2zim_AA[Alignment: 1 2]

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the structural change


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Function

EC*1

CSA distance*2

6.1.1.26

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

Ligand

PDB*1

Full name

2xPOP,2xYLY

2x(PYROPHOSPHATE 2-),2x((2R)-2-AMINO-6-({[(2S,3R)-3-METHYLPYRROLIDIN-2-YL]CARBNYL}AMINO)HEXANOYL [(2S,3R,4R,5R)-5-(6-AMINO-9H-PURIN--YL)-3,4-DIHYDROXYTETRAHYDROFURAN-2-YL]METHYL HYDROGEN(R)-PHOSPHATE)

*1 Ligand name designated by the PDB identifiers.

Segments

Component No.

Fixed*1

Moving*1

Motion type

Ligand binding

Coupled motion type

1

D1(188A-207A,212A-277A,287A-332A,338A-376A,388A-454A,188A-207A,212A-277A,287A-332A,338A-376A,388A-454A)

L2(377A-387A)

Local

Coupled

Closure

2

D1

L3(333A-337A)

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

5.7

+4

2

4

*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

0.76

2

0.2

*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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