ID.1

TRANSLATION INITIATION FACTOR IF2/EIF5B

PDB

The ligand-free form

1g7r_A [Alignment: 1]

The ligand-bound form

1g7t_A[Alignment: 1]

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Animations of

the structural change



Using Jmol

Function

EC*1

CSA distance*2

3.2

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

Ligand

PDB*1

Full name

GNP

PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER

*1 Ligand name designated by the PDB identifiers.

Segments

Component No.

Fixed*1

Moving*1

Motion type

Ligand binding

Coupled motion type

1

D1(3A-12A,19A-32A,40A-77A,85A-118A,122A-285A,295A-345A)

D2(78A-79A,82A-84A,119A-121A,346A-458A)

Domain

Independent

2

D2

D3(459A-558A,566A-583A)

Domain

Independent

3

D1

L4(13A-18A)

Local

Coupled

Closure

4

D1

L5(285A-285A,292A-294A)

Local

Independent

5

D2

L6(78A-84A)

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

1.4

2

1.6

3

Yes

+6

4

Yes

+2

5

4.1

+2

+2

*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

Free

Coupled

2

Bound

Coupled

3

4

5

Bound

Independent

*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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