CL.24

PHOSPHO-2-DEHYDRO-3-DEOXYHEPTONATE ALDOLASE

PDB

The ligand-free form

1ofp_AB [Alignment: 1 2]

The ligand-bound form

1of6_EF[Alignment: 1 2]

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Animations of

the structural change


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Function

EC*1

CSA distance*2

2.5.1.54

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

2xDTY,2xMN

2x(D-TYROSINE),2x(MANGANESE (II) 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(18E-110E,121E-202E,208E-249E,257E-280E,289E-322E,335E-368E,18F-110F,121F-250F,256F-281F,289F-326F,335F-368F)

L2(281E-288E)

Local

Coupled

Closure

2

D1

L3(250E-256E)

Local

Independent

3

D1

L4(327F-327F,330F-334F)

Local

Independent

4

D1

L5(203E-207E)

Local

Independent

5

D1

L6(323E-327E)

Local

Independent

6

D1

L7(251F-255F)

Local

Independent

7

D1

L8(111E-113E,119E-120E)

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

Yes

+8

2

Yes

+7

3

Yes

+6

4

Yes

+5

5

Yes

+5

6

Yes

+4

7

Yes

+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.

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