ID.47

DIPEPTIDYL PEPTIDASE IV

PDB

The ligand-free form

2i78_CD [Alignment: 1 2]

The ligand-bound form

1u8e_AB[Alignment: 1 2]

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Animations of

the structural change


Using Jmol

Function

EC*1

CSA distance*2

3.4.14.5

20.7

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

Ligand

PDB*1

Full name

11xNAG,5xNDG

11x(N-ACETYL-D-GLUCOSAMINE),5x(2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE)

*1 Ligand name designated by the PDB identifiers.

Segments

Component No.

Fixed*1

Moving*1

Motion type

Ligand binding

Coupled motion type

1

D1(41A-236A,252A-546A,548A-735A,743A-761A,239B-255B,702B-702B,726B-731B,734B-741B,754B-756B)

D2(237A-241A,244A-244A,248A-251A,736A-742A,762A-764A,39B-238B,256B-546B,548B-650B,658B-672B,674B-678B,690B-691B,699B-701B,703B-711B,716B-718B,720B-725B,732B-733B,742B-753B,757B-762B)

Domain

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

*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

*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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