CL.6

PHOSPHORIBOSYLFORMYLGLYCINAMIDINE SYNTHASE II

PDB

The ligand-free form

1vk3_A [Alignment: 1]

The ligand-bound form

2hs4_A[Alignment: 1]

View

Animations of

the structural change


Using Jmol

Function

EC*1

CSA distance*2

6.3.5.3

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

Ligand

PDB*1

Full name

ACP,FGR,2xMG

PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER,N-(N-FORMYLGLYCYL)-5-O-PHOSPHONO-BETA-D-RIBOFURANOSYLAINE,2x(MAGNESIUM 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(2A-48A,55A-186A,203A-361A,370A-603A)

L2(187A-202A)

Local

Coupled

Closure

2

D1

L3(362A-369A)

Local

Independent

3

D1

L4(49A-54A)

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

Yes

+16

2

4.8

3

6

*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

0.71

*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

2

Bound

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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