If you see this message after the page is completely loaded, then JavaScript is not supported or disabled in your browser. Please consider enabling JavaScript for this site.

DDL_STAAC_1_356

D-alanine--D-alanine ligase [D-alanine--D-alanine ligase family]

Composition of the binding site

Protein chains monomer [domain annotation]
A1 (DDL_STAAC):D: ATP-grasp (289, 310:313)
19, 20, 23, 92:96, 101, 117, 118
19, 20, 23, 92:96, 101, 117, 118, 289, 310:313

Full PDB list

2i80, 2i87, 2i8c, 3n8d (redundant Pocketome entry)

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1
V
1
9
S
2
0
F
9
2
P
9
3
L
9
4
L
9
5
H
9
6
V
1
1
7
G
1
1
8
L
2
8
9
M
3
1
0
P
3
1
1
G
3
1
2
F
3
1
3
[1]2i80.a g1l18 . . . . . . . . . . . . . .
[1]3n8d.b none . . . . . . - . . . . . . .

Legend

B backbone contact  S side chain contact  F BB + SCh
.
 no contact C covalent bond
X mutation to X * complex cases - deletion
M contact with cofactors/metals (if any)

Site contact map

[download in TSV format]
   
PDB.ch
A1
V
1
9
S
2
0
T
2
3
F
9
2
P
9
3
L
9
4
L
9
5
H
9
6
E
1
0
1
V
1
1
7
G
1
1
8
L
2
8
9
M
3
1
0
P
3
1
1
G
3
1
2
F
3
1
3
[1]2i80.a . . . . . . . . . . . . . . . .
[1]3n8d.b . . . . . . . - . . . . . . . .

Legend

B backbone contact  S side chain contact  F BB + SCh
.
 no contact C covalent bond
X X X X X  clash
X mutation to X * complex cases - deletion
M contact with cofactors/metals (if any)

Pocket-ligand steric compatibility

Ligands (x) vs pockets (y) colored by number of steric clashes

zoom: [−] [+]; [view as image]; [download as text]

pocketligand
≥10
9
8
7
6
5
4
3
2
1
0
2i80.a:g1l
3n8d.b is apo
[1] 2i80.a
0.1
-
[1] 3n8d.b 0.5
-
[Pocket-ligand steric clashes matrix]

Pocket clash dissimilarity (1 cluster)

Pockets (x) vs pockets (y) colored by ligand clash profile difference

zoom: [−] [+]; [view as image]; [download as text]

pocketpocket
≥1.
.9
.8
.7
.6
.5
.4
.3
.2
.1
.0
2i80.a
3n8d.b
[1] 2i80.a
0
.04
[1] 3n8d.b .04
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 1.2 Å)

Pockets (x) vs pockets (y) colored by RMSD of site residue backbone atoms

zoom: [−] [+]; [view as image]; [download as text]

pocketpocket
≥10 Å
9 Å
8 Å
7 Å
6 Å
5 Å
4 Å
3 Å
2 Å
1 Å
0 Å
2i80.a
3n8d.b
[1] 2i80.a
0
1.4
[1] 3n8d.b 1.4
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 0.7 Å)

Pockets (x) vs pockets (y) colored by RMSD of all site residue atoms

zoom: [−] [+]; [view as image]; [download as text]

pocketpocket
≥10 Å
9 Å
8 Å
7 Å
6 Å
5 Å
4 Å
3 Å
2 Å
1 Å
0 Å
2i80.a
3n8d.b
[1] 2i80.a
0
2.3
[1] 3n8d.b 2.3
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

L C X E | Background Color: | Anaglyph Stereo:

loading...