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_ENTFA_1_325

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

Composition of the binding site

Protein chains monomer
A1 (DNLJ_ENTFA):25, 26, 29, 30, 35, 37:39, 42, 43, 84:89, 91, 118:121, 125, 141, 173, 175, 202, 227, 228, 230, 289, 291, 303, 308, 310, 311, 31525, 26, 29, 30, 35, 37:39, 42, 43, 84:89, 91, 118:121, 125, 141, 173, 175, 202, 227, 228, 230, 289, 291, 303, 308, 310, 311, 315

Full PDB list

1ta8, 1tae, 3ba8, 3ba9, 3baa, 3bab, 4eeq, 4efb, 4efe, 4lh6, 4lh7

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1
Y
2
5
S
2
6
Y
2
9
Y
3
0
P
3
5
V
3
7
E
3
8
D
3
9
Y
4
2
D
4
3
I
8
4
P
8
5
M
8
6
Y
8
7
S
8
8
L
8
9
D
9
1
E
1
1
8
L
1
1
9
K
1
2
0
I
1
2
1
A
1
2
5
R
1
4
1
R
1
7
3
E
1
7
5
Y
2
2
7
T
2
2
8
V
2
8
9
K
2
9
1
F
3
0
3
P
3
0
8
W
3
1
0
A
3
1
1
K
3
1
5
[1]1ta8.a none . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]1tae.a nad44 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]3ba8.a 3b820 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]3ba9.a 3b932 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]3baa.a 3ba26 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]3bab.a 3bd30 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]4eeq.a 0ox16 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]4efb.a 0ow23 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]4efe.a 0ov23 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]4lh6.a 1x714 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]4lh7.a 1x816 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

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
2
5
S
2
6
Y
2
9
Y
3
0
P
3
5
V
3
7
E
3
8
D
3
9
Y
4
2
D
4
3
I
8
4
P
8
5
M
8
6
Y
8
7
S
8
8
L
8
9
D
9
1
E
1
1
8
L
1
1
9
K
1
2
0
I
1
2
1
A
1
2
5
R
1
4
1
R
1
7
3
E
1
7
5
R
2
0
2
Y
2
2
7
T
2
2
8
A
2
3
0
V
2
8
9
K
2
9
1
F
3
0
3
P
3
0
8
W
3
1
0
A
3
1
1
K
3
1
5
[1]1ta8.a . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]1tae.a . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]3ba8.a . . . . . . . . . . . . . . . . . . . . . . * . . . . . . . . . . . . .
[1]3ba9.a . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]3baa.a . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]3bab.a . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]4eeq.a . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]4efb.a . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]4efe.a . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]4lh6.a . . . . . . . . . . . . . * . . . . . . . . . . . . . . . . . . . . . .
[1]4lh7.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
1ta8.a is apo
1tae.a:nad
3ba8.a:3b8
3ba9.a:3b9
3baa.a:3ba
3bab.a:3bd
4eeq.a:0ox
4efb.a:0ow
4efe.a:0ov
4lh6.a:1x7
4lh7.a:1x8
[1] 1ta8.a
-
0 0.4 0.3 0.4 0.4 0.2 0.3 0.4 0.4 0.5
[1] 1tae.a -
0
0.1 0.1 0.2 0.9 0 0.1 0.1 0.2 0.3
[1] 3ba8.a - 1.3
0
0.1 0.6 1.7 0 1.6 0.2 0.4 0.7
[1] 3ba9.a - 0 0.1
0
0.1 0 0 0 0.1 0.3 0.6
[1] 3baa.a - 0.3 0 0.1
0
0 0.1 0.1 0.2 0.4 0.4
[1] 3bab.a - 0.4 0.1 0.1 0.5
0
0.1 0.1 0.1 0.5 0.7
[1] 4eeq.a - 0.1 0.1 0.1 0.2 0.1
0
0 0 0.2 0.4
[1] 4efb.a - 0.2 0.2 0.1 0.2 0.5 0
0
0 0.2 0.6
[1] 4efe.a - 0 0.1 0.1 0.1 0.1 0 0
0
0.2 0.5
[1] 4lh6.a - 0.5 2.6 2.9 1.7 1.8 1.3 1.4 2.1
0
0.3
[1] 4lh7.a - 0.8 3.0 1.6 1.6 1.9 1.1 1.4 2.0 0
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
1ta8.a
1tae.a
3ba8.a
3ba9.a
3baa.a
3bab.a
4eeq.a
4efb.a
4efe.a
4lh6.a
4lh7.a
[1] 1ta8.a
0
.03 .07 .01 .02 .03 .02 .04 .02 .10 .11
[1] 1tae.a .03
0
.05 .04 .04 .06 .04 .03 .04 .12 .14
[1] 3ba8.a .07 .05
0
.07 .06 .07 .06 .04 .05 .15 .17
[1] 3ba9.a .01 .04 .07
0
.02 .03 .03 .04 .03 .10 .12
[1] 3baa.a .02 .04 .06 .02
0
.03 .03 .03 .02 .09 .12
[1] 3bab.a .03 .06 .07 .03 .03
0
.04 .04 .03 .12 .14
[1] 4eeq.a .02 .04 .06 .03 .03 .04
0
.02 .01 .10 .12
[1] 4efb.a .04 .03 .04 .04 .03 .04 .02
0
.02 .11 .13
[1] 4efe.a .02 .04 .05 .03 .02 .03 .01 .02
0
.11 .13
[1] 4lh6.a .10 .12 .15 .10 .09 .12 .10 .11 .11
0
.03
[1] 4lh7.a .11 .14 .17 .12 .12 .14 .12 .13 .13 .03
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 0.7 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
1ta8.a
1tae.a
3ba8.a
3ba9.a
3baa.a
3bab.a
4eeq.a
4efb.a
4efe.a
4lh6.a
4lh7.a
[1] 1ta8.a
0
22 0.4 0.3 0.2 0.4 0.3 0.4 0.2 2.0 2.3
[1] 1tae.a 22
0
22 22 22 22 22 22 22 23 23
[1] 3ba8.a 0.4 22
0
0.3 0.3 0.3 0.3 0.3 0.3 2.0 2.4
[1] 3ba9.a 0.3 22 0.3
0
0.3 0.3 0.3 0.3 0.3 2.0 2.3
[1] 3baa.a 0.2 22 0.3 0.3
0
0.3 0.3 0.4 0.2 2.0 2.4
[1] 3bab.a 0.4 22 0.3 0.3 0.3
0
0.4 0.4 0.4 2.1 2.4
[1] 4eeq.a 0.3 22 0.3 0.3 0.3 0.4
0
0.2 0.2 2.0 2.3
[1] 4efb.a 0.4 22 0.3 0.3 0.4 0.4 0.2
0
0.3 1.9 2.2
[1] 4efe.a 0.2 22 0.3 0.3 0.2 0.4 0.2 0.3
0
2.0 2.3
[1] 4lh6.a 2.0 23 2.0 2.0 2.0 2.1 2.0 1.9 2.0
0
0.4
[1] 4lh7.a 2.3 23 2.4 2.3 2.4 2.4 2.3 2.2 2.3 0.4
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 0.4 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
1ta8.a
1tae.a
3ba8.a
3ba9.a
3baa.a
3bab.a
4eeq.a
4efb.a
4efe.a
4lh6.a
4lh7.a
[1] 1ta8.a
0
22 0.7 0.6 0.6 0.6 0.4 0.6 0.4 2.5 2.8
[1] 1tae.a 22
0
22 22 22 22 22 22 22 23 23
[1] 3ba8.a 0.7 22
0
0.7 0.6 0.7 0.7 0.6 0.7 2.5 2.8
[1] 3ba9.a 0.6 22 0.7
0
0.6 0.6 0.6 0.6 0.6 2.5 2.7
[1] 3baa.a 0.6 22 0.6 0.6
0
0.5 0.5 0.6 0.5 2.5 2.8
[1] 3bab.a 0.6 22 0.7 0.6 0.5
0
0.6 0.6 0.6 2.6 2.8
[1] 4eeq.a 0.4 22 0.7 0.6 0.5 0.6
0
0.4 0.2 2.5 2.8
[1] 4efb.a 0.6 22 0.6 0.6 0.6 0.6 0.4
0
0.4 2.4 2.7
[1] 4efe.a 0.4 22 0.7 0.6 0.5 0.6 0.2 0.4
0
2.5 2.8
[1] 4lh6.a 2.5 23 2.5 2.5 2.5 2.6 2.5 2.4 2.5
0
0.6
[1] 4lh7.a 2.8 23 2.8 2.7 2.8 2.8 2.8 2.7 2.8 0.6
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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

loading...