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DNLJ_HAEIN_64_324

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

Composition of the binding site

Protein chains monomer
A1 (DNLJ_HAEIN):77:82, 114:117, 119, 121, 137, 172, 174, 201, 226, 289, 291, 303, 308, 310, 31177:82, 114:117, 119, 121, 137, 172, 174, 201, 226, 289, 291, 303, 308, 310, 311

Full PDB list

3bac, 3pn1, 3uq8, 4uco, 4ucr, 4ucs, 4uct, 4ucu, 4ucv, 4ufz

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1
I
7
7
P
7
8
L
8
0
S
8
1
L
8
2
E
1
1
4
P
1
1
5
K
1
1
6
L
1
1
7
G
1
1
9
A
1
2
1
R
1
3
7
E
1
7
4
R
2
0
1
Y
2
2
6
V
2
8
9
K
2
9
1
F
3
0
3
P
3
0
8
[1]3bac.a 3b932 . . . . . . . . . . . . . . . . . . .
[1]3pn1.a ivh24 . . . . . . . . . . . . . . . . . . .
[1]3uq8.a amp22 . . . . . . . * . . . . . . . . . . .
[1]4uco.a d4123 . . . . . . . . . . . . . . . . . . .
[1]4ucr.a jcf15 . . . . . . . . . . . . . . . . . . .
[1]4ucs.a 9mj14 . . . . . . . . . . . . . . . . . . .
[1]4uct.a 5u115 . . . . . . . . . . . . . . . . . . .
[1]4ucu.a 8hc14 . . . . . . . . . . . . . . . . . . .
[1]4ucv.a i6g15 . . . . . . . . . . . . . . . . . . .
[1]4ufz.a ia723 . . . . . . . . . . . . . . . . . . .

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

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PDB.ch
A1
I
7
7
P
7
8
M
7
9
L
8
0
S
8
1
L
8
2
E
1
1
4
P
1
1
5
K
1
1
6
L
1
1
7
G
1
1
9
A
1
2
1
R
1
3
7
R
1
7
2
E
1
7
4
R
2
0
1
Y
2
2
6
V
2
8
9
K
2
9
1
F
3
0
3
P
3
0
8
W
3
1
0
A
3
1
1
[1]3bac.a . . . . . . . . . . . . . . . . . . . . . . .
[1]3pn1.a . . . . . . . . . . . . . . . . . . . . . . .
[1]3uq8.a . . . . . . . . * . . . . . . . . . . . . . .
[1]4uco.a . . . . . . . . . . . . . . . . . . . . . . .
[1]4ucr.a . . . . . . . . . . . . * . . . . . . . . . .
[1]4ucs.a . . . . . . . . . . . . . . . . . . . . . . .
[1]4uct.a . . . . . . . . * . . . . . . . . . . . . . .
[1]4ucu.a . . . . . . * . . . . . . . . . . . . . . . .
[1]4ucv.a . . . . . . * . . . . . . . . . . . . . . . .
[1]4ufz.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

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pocketligand
≥10
9
8
7
6
5
4
3
2
1
0
3bac.a:3b9
3pn1.a:ivh
3uq8.a:amp
4uco.a:d41
4ucr.a:jcf
4ucs.a:9mj
4uct.a:5u1
4ucu.a:8hc
4ucv.a:i6g
4ufz.a:ia7
[1] 3bac.a
0
0.2 0.2 0.2 0.2 0 0 0.2 0.2 0
[1] 3pn1.a 0.2
0
0.3 0.2 0.4 0.1 0 0.2 0.2 0.1
[1] 3uq8.a 0.2 1.0
0.4
0.9 0.9 0.3 0 0.2 0.1 0.3
[1] 4uco.a 0 0.3 0.6
0
0.2 0 0 0.3 0.5 0.1
[1] 4ucr.a 1.1 2.2 2.5 1.7
0
0.3 0.5 0.1 0.3 2.2
[1] 4ucs.a 0.8 0.8 1.6 0.1 0.4
0
0.4 0.5 0.6 0.8
[1] 4uct.a 0.8 1.3 0.4 0.6 1.2 0.8
0
0.1 0.1 0.1
[1] 4ucu.a 0.6 1.2 0.3 1.0 0.7 0.8 0.4
0
0.1 0.7
[1] 4ucv.a 1.0 1.0 0.5 0.9 0.7 1.1 0.4 0
0
0.8
[1] 4ufz.a 0 0.3 0.2 0.1 0 0 0 0.2 0.1
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
3bac.a
3pn1.a
3uq8.a
4uco.a
4ucr.a
4ucs.a
4uct.a
4ucu.a
4ucv.a
4ufz.a
[1] 3bac.a
0
.02 .05 .03 .16 .10 .06 .08 .10 .01
[1] 3pn1.a .02
0
.07 .04 .15 .10 .08 .08 .09 .02
[1] 3uq8.a .05 .07
0
.08 .18 .14 .05 .12 .14 .06
[1] 4uco.a .03 .04 .08
0
.14 .09 .07 .08 .10 .02
[1] 4ucr.a .16 .15 .18 .14
0
.12 .18 .15 .15 .14
[1] 4ucs.a .10 .10 .14 .09 .12
0
.15 .14 .14 .10
[1] 4uct.a .06 .08 .05 .07 .18 .15
0
.10 .13 .06
[1] 4ucu.a .08 .08 .12 .08 .15 .14 .10
0
.06 .07
[1] 4ucv.a .10 .09 .14 .10 .15 .14 .13 .06
0
.09
[1] 4ufz.a .01 .02 .06 .02 .14 .10 .06 .07 .09
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 1.4 Å)

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

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pocketpocket
≥10 Å
9 Å
8 Å
7 Å
6 Å
5 Å
4 Å
3 Å
2 Å
1 Å
0 Å
3bac.a
3pn1.a
3uq8.a
4uco.a
4ucr.a
4ucs.a
4uct.a
4ucu.a
4ucv.a
4ufz.a
[1] 3bac.a
0
8.7 8.6 7.2 7.0 7.1 7.3 7.2 7.3 7.3
[1] 3pn1.a 8.7
0
1.0 6.2 6.2 6.2 6.2 6.3 6.3 6.2
[1] 3uq8.a 8.6 1.0
0
6.1 6.2 6.2 6.2 6.2 6.3 6.2
[1] 4uco.a 7.2 6.2 6.1
0
0.5 0.6 0.4 0.5 0.5 0.5
[1] 4ucr.a 7.0 6.2 6.2 0.5
0
0.4 0.7 0.7 0.6 0.7
[1] 4ucs.a 7.1 6.2 6.2 0.6 0.4
0
0.8 0.9 0.8 0.9
[1] 4uct.a 7.3 6.2 6.2 0.4 0.7 0.8
0
0.3 0.3 0.2
[1] 4ucu.a 7.2 6.3 6.2 0.5 0.7 0.9 0.3
0
0.3 0.2
[1] 4ucv.a 7.3 6.3 6.3 0.5 0.6 0.8 0.3 0.3
0
0.3
[1] 4ufz.a 7.3 6.2 6.2 0.5 0.7 0.9 0.2 0.2 0.3
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 0.9 Å)

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

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pocketpocket
≥10 Å
9 Å
8 Å
7 Å
6 Å
5 Å
4 Å
3 Å
2 Å
1 Å
0 Å
3bac.a
3pn1.a
3uq8.a
4uco.a
4ucr.a
4ucs.a
4uct.a
4ucu.a
4ucv.a
4ufz.a
[1] 3bac.a
0
8.7 8.7 7.1 7.0 7.0 7.2 7.1 7.2 7.1
[1] 3pn1.a 8.7
0
1.6 7.4 7.4 7.4 7.4 7.4 7.5 7.5
[1] 3uq8.a 8.7 1.6
0
7.3 7.4 7.4 7.4 7.4 7.5 7.4
[1] 4uco.a 7.1 7.4 7.3
0
1.0 0.9 0.8 1.2 1.0 0.7
[1] 4ucr.a 7.0 7.4 7.4 1.0
0
0.9 1.2 1.3 1.2 1.1
[1] 4ucs.a 7.0 7.4 7.4 0.9 0.9
0
1.1 1.4 1.2 1.2
[1] 4uct.a 7.2 7.4 7.4 0.8 1.2 1.1
0
1.0 1.0 0.8
[1] 4ucu.a 7.1 7.4 7.4 1.2 1.3 1.4 1.0
0
0.9 1.1
[1] 4ucv.a 7.2 7.5 7.5 1.0 1.2 1.2 1.0 0.9
0
1.0
[1] 4ufz.a 7.1 7.5 7.4 0.7 1.1 1.2 0.8 1.1 1.0
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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