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4CL2_TOBAC_1_542

4-coumarate--CoA ligase 2 [ATP-dependent AMP-binding enzyme family]

Composition of the binding site

Protein chains monomer
A1 (4CL2_TOBAC):189:193, 197, 237:239, 243, 306:311, 331:336, 340, 341, 344, 360, 420, 432, 435, 437, 439, 441, 446, 526189:193, 197, 237:239, 243, 306:311, 331:336, 340, 341, 344, 360, 420, 432, 435, 437, 439, 441, 446, 526

Full PDB list

5bsm, 5bsr, 5bst, 5bsu, 5bsv, 5bsw, 5u95 (redundant Pocketome entry)

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1
S
1
8
9
S
1
9
0
G
1
9
1
T
1
9
2
T
1
9
3
K
1
9
7
H
2
3
7
Y
2
3
9
S
2
4
3
M
3
0
6
S
3
0
7
G
3
0
8
A
3
0
9
A
3
1
0
P
3
1
1
Q
3
3
1
G
3
3
2
Y
3
3
3
G
3
3
4
M
3
3
5
T
3
3
6
P
3
4
0
V
3
4
1
M
3
4
4
C
3
6
0
D
4
2
0
I
4
3
2
R
4
3
5
K
4
3
7
K
4
4
1
Q
4
4
6
K
5
2
6
[1]5bsm.a atp,mg32 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]5bsr.a amp23 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]5bst.a 4uu34 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]5bsu.a 4uv35 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]5bsv.a 4uw36 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]5u95.b none . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

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
S
1
8
9
S
1
9
0
G
1
9
1
T
1
9
2
T
1
9
3
K
1
9
7
H
2
3
7
I
2
3
8
Y
2
3
9
S
2
4
3
M
3
0
6
S
3
0
7
G
3
0
8
A
3
0
9
A
3
1
0
P
3
1
1
Q
3
3
1
G
3
3
2
Y
3
3
3
G
3
3
4
M
3
3
5
T
3
3
6
P
3
4
0
V
3
4
1
M
3
4
4
C
3
6
0
D
4
2
0
I
4
3
2
R
4
3
5
K
4
3
7
L
4
3
9
K
4
4
1
Q
4
4
6
K
5
2
6
[1]5bsm.a . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]5bsr.a . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . * . * .
[1]5bst.a . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . * . . .
[1]5bsu.a . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . * .
[1]5bsv.a . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . * . . .
[1]5u95.b . * . . . . . . . . . . . . . . . . . . . . . . . . . . * . . . . .

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
5bsm.a:atp,mg
5bsr.a:amp
5bst.a:4uu
5bsu.a:4uv
5bsv.a:4uw
5u95.b is apo
[1] 5bsm.a
0.1
0.5 1.0 1.2 1.4 -
[1] 5bsr.a 3.0
0
0.4 0.4 0.4 -
[1] 5bst.a 2.7 0.3
0
0.2 0.8 -
[1] 5bsu.a 2.5 0.2 0
0.1
0.5 -
[1] 5bsv.a 2.8 0.3 0.1 0.1
0.1
-
[1] 5u95.b 3.2 2.2 2.5 2.6 2.7
-
[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
5bsm.a
5bsr.a
5bst.a
5bsu.a
5bsv.a
5u95.b
[1] 5bsm.a
0
.13 .13 .13 .13 .14
[1] 5bsr.a .13
0
.05 .04 .03 .19
[1] 5bst.a .13 .05
0
.03 .02 .20
[1] 5bsu.a .13 .04 .03
0
.03 .21
[1] 5bsv.a .13 .03 .02 .03
0
.19
[1] 5u95.b .14 .19 .20 .21 .19
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 3.4 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
5bsm.a
5bsr.a
5bst.a
5bsu.a
5bsv.a
5u95.b
[1] 5bsm.a
0
7.7 7.6 7.6 7.6 6.9
[1] 5bsr.a 7.7
0
0.7 0.7 0.6 5.1
[1] 5bst.a 7.6 0.7
0
0.2 0.3 5.2
[1] 5bsu.a 7.6 0.7 0.2
0
0.1 5.2
[1] 5bsv.a 7.6 0.6 0.3 0.1
0
5.2
[1] 5u95.b 6.9 5.1 5.2 5.2 5.2
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 2.9 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
5bsm.a
5bsr.a
5bst.a
5bsu.a
5bsv.a
5u95.b
[1] 5bsm.a
0
8.3 8.2 8.2 8.2 7.6
[1] 5bsr.a 8.3
0
1.1 1.1 1.1 5.8
[1] 5bst.a 8.2 1.1
0
0.3 0.5 5.9
[1] 5bsu.a 8.2 1.1 0.3
0
0.4 5.9
[1] 5bsv.a 8.2 1.1 0.5 0.4
0
5.9
[1] 5u95.b 7.6 5.8 5.9 5.9 5.9
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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