ID.67

OUTER PROTEIN YOPM

PDB

The ligand-free form

1g9u_A [Alignment: 1]

The ligand-bound form

1jl5_A[Alignment: 1]

View

Animations of

the structural change


Using Jmol

Ligand

PDB*1

Full name

2xCA

2x(CALCIUM 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(1056A-1056A,1079A-1082A,1093A-1093A,1095A-1100A,1111A-1114A,1131A-1139A,1151A-1160A,1165A-1171A,1173A-1181A,1184A-1382A)

D2(1042A-1055A,1057A-1078A,1083A-1092A,1094A-1094A,1101A-1110A,1115A-1130A,1140A-1150A,1161A-1164A,1172A-1172A,1182A-1183A)

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

1.2

*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

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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