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DNLJ_ECOLI_1_586

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

Composition of the binding site

Protein chains monomer
A1 (DNLJ_ECOLI):15, 16, 18, 19, 22, 23, 28, 30:32, 35, 36, 80:82, 113:116, 120, 136, 173, 225, 288, 290, 305, 307, 309, 314, 379, 381, 383, 38415, 16, 18, 19, 22, 23, 28, 30:32, 35, 36, 80:82, 113:116, 120, 136, 173, 225, 288, 290, 305, 307, 309, 314, 379, 381, 383, 384

Full PDB list

2owo, 4glx, 5tt5

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1
H
1
8
E
1
9
Y
2
2
H
2
3
P
2
8
I
3
0
P
3
1
D
3
2
Y
3
5
D
3
6
L
8
0
S
8
1
L
8
2
E
1
1
3
L
1
1
4
K
1
1
5
L
1
1
6
A
1
2
0
R
1
3
6
E
1
7
3
Y
2
2
5
V
2
8
8
K
2
9
0
P
3
0
7
W
3
0
9
K
3
1
4
V
3
8
3
I
3
8
4
[1]2owo.a ampC42 . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]4glx.a 0xs,C39 . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]5tt5.a mg,nad45 . . . . . . . . . . . . . . . M . . . . . . . . . . . .

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
1
5
R
1
6
H
1
8
E
1
9
Y
2
2
H
2
3
P
2
8
I
3
0
P
3
1
D
3
2
Y
3
5
D
3
6
L
8
0
S
8
1
L
8
2
E
1
1
3
L
1
1
4
K
1
1
5
L
1
1
6
A
1
2
0
R
1
3
6
E
1
7
3
Y
2
2
5
V
2
8
8
K
2
9
0
R
3
0
5
P
3
0
7
W
3
0
9
K
3
1
4
R
3
7
9
G
3
8
1
V
3
8
3
I
3
8
4
[1]2owo.a . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . * .
[1]4glx.a . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . * .
[1]5tt5.a . . . * . . . . . . * . . . . . . M . . . . . . . . . . . . . . .

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

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pocketligand
≥10
9
8
7
6
5
4
3
2
1
0
2owo.a:ampC
4glx.a:0xs,C
5tt5.a:mg,nad
[1] 2owo.a
0
0 2.0
[1] 4glx.a 0.4
0
1.9
[1] 5tt5.a 6.0 5.1
0
[Pocket-ligand steric clashes matrix]

Pocket clash dissimilarity (1 cluster)

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

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pocketpocket
≥1.
.9
.8
.7
.6
.5
.4
.3
.2
.1
.0
2owo.a
4glx.a
5tt5.a
[1] 2owo.a
0
.02 .24
[1] 4glx.a .02
0
.23
[1] 5tt5.a .24 .23
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 0.5 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
2owo.a
4glx.a
5tt5.a
[1] 2owo.a
0
0.4 22
[1] 4glx.a 0.4
0
22
[1] 5tt5.a 22 22
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
2owo.a
4glx.a
5tt5.a
[1] 2owo.a
0
0.5 23
[1] 4glx.a 0.5
0
24
[1] 5tt5.a 23 24
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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