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.

DNLJ_STAAU_1_312

DNA ligase [NAD-dependent DNA ligase family. LigA subfamily]

Composition of the binding site

Protein chains monomer
A1 (DNLJ_STAAU):80, 82, 110:113, 133, 167, 219, 281, 283, 300, 30380, 82, 110:113, 133, 167, 219, 281, 283, 300, 303

Full PDB list

3jsl, 3jsn, 4cc5, 4cc6, 5fpo, 5fpr (redundant Pocketome entry)

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1
L
8
0
L
8
2
E
1
1
0
L
1
1
1
K
1
1
2
I
1
1
3
R
1
3
3
E
1
6
7
Y
2
1
9
V
2
8
1
K
2
8
3
P
3
0
0
A
3
0
3
[1]3jsl.a none . . . . . . . . . . . . .
[1]4cc5.a l5v12 . . . . . . . . . . . . .
[1]4cc6.a l5y23 . . . . . . . . . . . . .
[1]5fpo.a 10l10 . . . . . . . . . . . . .

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
L
8
0
L
8
2
E
1
1
0
L
1
1
1
K
1
1
2
I
1
1
3
R
1
3
3
E
1
6
7
Y
2
1
9
V
2
8
1
K
2
8
3
P
3
0
0
A
3
0
3
[1]3jsl.a . . . . . . . . . . . . .
[1]4cc5.a . . . . . . . . . . . . .
[1]4cc6.a . . . . . . . . . . . . .
[1]5fpo.a . . . . . . . . . . . . .

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
3jsl.a is apo
4cc5.a:l5v
4cc6.a:l5y
5fpo.a:10l
[1] 3jsl.a
-
0.7 0.7 0
[1] 4cc5.a -
0
0 0
[1] 4cc6.a - 0.2
0
0
[1] 5fpo.a - 0.8 0.4
0
[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
3jsl.a
4cc5.a
4cc6.a
5fpo.a
[1] 3jsl.a
0
.09 .08 .02
[1] 4cc5.a .09
0
.02 .08
[1] 4cc6.a .08 .02
0
.07
[1] 5fpo.a .02 .08 .07
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 0.6 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
3jsl.a
4cc5.a
4cc6.a
5fpo.a
[1] 3jsl.a
0
0.2 0.4 0.2
[1] 4cc5.a 0.2
0
0.4 0.2
[1] 4cc6.a 0.4 0.4
0
0.3
[1] 5fpo.a 0.2 0.2 0.3
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 0.2 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
3jsl.a
4cc5.a
4cc6.a
5fpo.a
[1] 3jsl.a
0
0.7 0.8 0.5
[1] 4cc5.a 0.7
0
0.6 0.5
[1] 4cc6.a 0.8 0.6
0
0.7
[1] 5fpo.a 0.5 0.5 0.7
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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

loading...