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IEMT_CLABR_1_368

(Iso)eugenol O-methyltransferase [Class I-like SAM-binding methyltransferase superfamily. Cation-independent O- methyltransferase family. COMT subfamily]

Composition of the binding site

Protein chains homodimer
A1 (IEMT_CLABR):130, 133, 134, 139, 165, 166, 169, 179, 183, 269, 272, 273, 319, 322, 323, 326:328130, 133, 134, 139, 165, 166, 169, 179, 183, 269, 272, 273, 319, 322, 323, 326:328
A2 (IEMT_CLABR):3030
Cofactors (cF):sah

Full PDB list

3reo, 3tky, 5cvj, 5cvu, 5cvv

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1 A2 cF
F
1
3
0
T
1
3
3
A
1
3
4
L
1
3
9
E
1
6
5
F
1
6
6
F
1
7
9
M
1
8
3
W
2
6
9
H
2
7
2
D
2
7
3
T
3
1
9
L
3
2
2
M
3
2
3
Y
3
2
6
N
3
2
7
P
3
2
8
S
3
0
[1]3reo.a none . L . . I . . . . . . . . . . . . . sah
[1]3reo.b eug12 . L . . I . . . . . . . . . . . . . sah
[1]3tky.a n7i13 . L . . I . . . . . . . . . . . . . sah
[1]5cvj.d n7i13 . L . . I W . . . . . . . . . . . .
[1]5cvu.a 55b15 . L . . I W . . . . . . . . . . . .
[1]5cvv.a n7i13 . L . . I W . . . . . M . . . . . R
[1]5cvv.b none . L . . I W . . . . . M . . . . . R

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 A2 cF
F
1
3
0
T
1
3
3
A
1
3
4
L
1
3
9
E
1
6
5
F
1
6
6
H
1
6
9
F
1
7
9
M
1
8
3
W
2
6
9
H
2
7
2
D
2
7
3
T
3
1
9
L
3
2
2
M
3
2
3
Y
3
2
6
N
3
2
7
P
3
2
8
S
3
0
[1]3reo.a . L . . I . . . . . . . . . . . * . . sah
[1]3reo.b . L . * I . . . . . . . . . . . * . . sah
[1]3tky.a . L . * I . . . . . . . . . . . . . . sah
[1]5cvj.d . L . . I W F . . . . . . . . . * . .
[1]5cvu.a . L . . I W F . . . . . . . . . * . .
[1]5cvv.a . L . . I W F . . . . . M . . . * . R
[1]5cvv.b . L . . I W F . . . . . M . . . * . R

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
3reo.a is apo
3reo.b:eug
3tky.a:n7i
5cvj.d:n7i
5cvu.a:55b
5cvv.a:n7i
5cvv.b is apo
[1] 3reo.a
-
0.1 3.0 0.2 0.6 1.0 -
[1] 3reo.b -
0
3.2 0.1 0.3 0.9 -
[1] 3tky.a - 0.2
0.2
0.1 0.1 0.5 -
[1] 5cvj.d - 0 3.2
0.1
0.2 0.5 -
[1] 5cvu.a - 0.1 2.4 0.1
0
0 -
[1] 5cvv.a - 0.7 2.8 0.6 1.5
0.3
-
[1] 5cvv.b - 0.9 3.5 1.1 1.9 0.6
-
[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
3reo.a
3reo.b
3tky.a
5cvj.d
5cvu.a
5cvv.a
5cvv.b
[1] 3reo.a
0
.04 .23 .06 .11 .19 .22
[1] 3reo.b .04
0
.22 .08 .13 .21 .23
[1] 3tky.a .23 .22
0
.22 .18 .25 .29
[1] 5cvj.d .06 .08 .22
0
.07 .16 .16
[1] 5cvu.a .11 .13 .18 .07
0
.09 .16
[1] 5cvv.a .19 .21 .25 .16 .09
0
.06
[1] 5cvv.b .22 .23 .29 .16 .16 .06
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 0.8 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
3reo.a
3reo.b
3tky.a
5cvj.d
5cvu.a
5cvv.a
5cvv.b
[1] 3reo.a
0
0.2 0.4 0.3 0.3 0.4 0.6
[1] 3reo.b 0.2
0
0.4 0.3 0.2 0.3 0.5
[1] 3tky.a 0.4 0.4
0
0.5 0.4 0.5 0.6
[1] 5cvj.d 0.3 0.3 0.5
0
0.3 0.4 0.5
[1] 5cvu.a 0.3 0.2 0.4 0.3
0
0.3 0.4
[1] 5cvv.a 0.4 0.3 0.5 0.4 0.3
0
0.3
[1] 5cvv.b 0.6 0.5 0.6 0.5 0.4 0.3
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 0.3 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
3reo.a
3reo.b
3tky.a
5cvj.d
5cvu.a
5cvv.a
5cvv.b
[1] 3reo.a
0
0.4 1.2 0.8 0.9 0.9 1.1
[1] 3reo.b 0.4
0
1.2 0.8 0.9 0.9 1.1
[1] 3tky.a 1.2 1.2
0
1.3 1.3 1.4 1.5
[1] 5cvj.d 0.8 0.8 1.3
0
0.7 0.5 0.8
[1] 5cvu.a 0.9 0.9 1.3 0.7
0
0.6 0.7
[1] 5cvv.a 0.9 0.9 1.4 0.5 0.6
0
0.6
[1] 5cvv.b 1.1 1.1 1.5 0.8 0.7 0.6
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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

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