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_HAEIN_1_64

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

Composition of the binding site

Protein chains monomer
A1 (DNLJ_HAEIN):18, 22, 23, 28, 30:32, 35, 36, 39, 40, 43, 59, 15418, 22, 23, 28, 30:32, 35, 36, 39, 40, 43, 59, 154

Full PDB list

3pn1, 3uq8, 4uco, 4ucr, 4ucs, 4uct, 4ucu, 4ucv, 4ufz (redundant Pocketome entry)

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1
Y
1
8
Y
2
2
P
2
8
V
3
0
P
3
1
D
3
2
Y
3
5
D
3
6
F
3
9
H
4
0
K
4
3
R
1
5
4
[1]3uq8.a nad44 . . . . . . . . . . . .
[1]4ucs.a iwh19 . . . . . . . . . . . .

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
Y
1
8
Y
2
2
H
2
3
P
2
8
V
3
0
P
3
1
D
3
2
Y
3
5
D
3
6
F
3
9
H
4
0
K
4
3
T
5
9
R
1
5
4
[1]3uq8.a . . . . . . . . . . . . . .
[1]4ucs.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
3uq8.a:nad
4ucs.a:iwh
[1] 3uq8.a
0
0.7
[1] 4ucs.a 2.9
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
3uq8.a
4ucs.a
[1] 3uq8.a
0
.16
[1] 4ucs.a .16
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
3uq8.a
4ucs.a
[1] 3uq8.a
0
0.3
[1] 4ucs.a 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
3uq8.a
4ucs.a
[1] 3uq8.a
0
1.1
[1] 4ucs.a 1.1
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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

loading...