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ANM3_HUMAN_209_531

Protein arginine N-methyltransferase 3 [Class I-like SAM-binding methyltransferase superfamily. Protein arginine N- methyltransferase family]

Composition of the binding site

Protein chains monomer [domain annotation]
A1 (ANM3_HUMAN):D: SAM-dependent MTase PRMT-type (370, 372, 375, 376, 379, 403, 405, 407, 449, 450, 484, 486)370, 372, 375, 376, 379, 403, 405, 407, 449, 450, 484, 486

Full PDB list

1f3l, 2fyt, 3smq, 4hsg, 4qqn, 4ryl

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1
V
3
7
0
D
3
7
2
K
3
7
5
H
3
7
6
R
3
7
9
V
4
0
3
E
4
0
5
L
4
0
7
T
4
4
9
A
4
5
0
V
4
8
4
L
4
8
6
[1]3smq.a tdu21 . . . . . . . . . . . .
[1]4hsg.a ktd22 . . . . . . . . . . . .
[1]4qqn.a 3bq24 . . . . . . . . . . . .
[1]4ryl.a 3zg22 . . . . . . . . . . . .
[2]1f3l.a none . . . . . . . V . . I .
[2]2fyt.a 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
V
3
7
0
D
3
7
2
K
3
7
5
H
3
7
6
R
3
7
9
V
4
0
3
E
4
0
5
L
4
0
7
T
4
4
9
A
4
5
0
V
4
8
4
L
4
8
6
[1]3smq.a . . . . . . . . . . . .
[1]4hsg.a . . . . . . . . . . . .
[1]4qqn.a . . . . . . . . . . . .
[1]4ryl.a . . . . . . . . . . . .
[2]1f3l.a . . . . * . . V . . I .
[2]2fyt.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
3smq.a:tdu
4hsg.a:ktd
4qqn.a:3bq
4ryl.a:3zg
1f3l.a is apo
2fyt.a is apo
[1] 3smq.a
0.1
0 0 0 - -
[1] 4hsg.a 0
0
0 0 - -
[1] 4qqn.a 0.1 0
0
0 - -
[1] 4ryl.a 0.1 0 0.1
0
- -
[2] 1f3l.a 2.8 3.0 2.6 3.0
-
-
[2] 2fyt.a 2.9 2.7 3.3 3.3 -
-
[Pocket-ligand steric clashes matrix]

Pocket clash dissimilarity (2 clusters)

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
3smq.a
4hsg.a
4qqn.a
4ryl.a
1f3l.a
2fyt.a
[1] 3smq.a
0
.01 0 0 .25 .27
[1] 4hsg.a .01
0
.01 .01 .26 .28
[1] 4qqn.a 0 .01
0
0 .25 .27
[1] 4ryl.a 0 .01 0
0
.25 .27
[2] 1f3l.a .25 .26 .25 .25
0
.10
[2] 2fyt.a .27 .28 .27 .27 .10
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

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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
3smq.a
4hsg.a
4qqn.a
4ryl.a
1f3l.a
2fyt.a
[1] 3smq.a
0
0.1 0.1 0.1 0.6 0.6
[1] 4hsg.a 0.1
0
0.1 0.1 0.6 0.6
[1] 4qqn.a 0.1 0.1
0
0.1 0.6 0.6
[1] 4ryl.a 0.1 0.1 0.1
0
0.6 0.6
[2] 1f3l.a 0.6 0.6 0.6 0.6
0
0.3
[2] 2fyt.a 0.6 0.6 0.6 0.6 0.3
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 0.2 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
3smq.a
4hsg.a
4qqn.a
4ryl.a
1f3l.a
2fyt.a
[1] 3smq.a
0
0.3 0.2 0.4 1.1 1.2
[1] 4hsg.a 0.3
0
0.2 0.4 1.2 1.3
[1] 4qqn.a 0.2 0.2
0
0.3 1.2 1.3
[1] 4ryl.a 0.4 0.4 0.3
0
1.2 1.3
[2] 1f3l.a 1.1 1.2 1.2 1.2
0
1.0
[2] 2fyt.a 1.2 1.3 1.3 1.3 1.0
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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