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ANM6_HUMAN_5_375

Protein arginine N-methyltransferase 6 [Class I-like SAM-binding methyltransferase superfamily. Protein arginine N- methyltransferase family. PRMT6 subfamily]

Composition of the binding site

Protein chains monomer [domain annotation]
A1 (ANM6_HUMAN):D: SAM-dependent MTase PRMT-type (162, 165, 168, 172, 264, 267, 268, 270, 271, 343:345, 350:353)
40
40, 162, 165, 168, 172, 264, 267, 268, 270, 271, 343:345, 350:353
Cofactors (cF):sah

Full PDB list

4hc4, 4qpp, 4qqk, 4y2h, 4y30, 5e8r, 5egs, 5hzm, 5wcf (redundant Pocketome entry)

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1 cF
L
1
6
2
S
1
6
5
S
1
6
8
E
2
6
4
L
2
6
7
E
2
6
8
L
3
4
3
L
3
4
4
P
3
4
5
P
3
5
0
R
3
5
1
R
3
5
2
L
3
5
3
[1]4qpp.b 36s26 . . . . . . . . . . . . .
[1]4y2h.b none . . . . . . . . . . . . . sah
[1]4y30.b none . . . . . Q . . . . . . . sah
[1]5egs.c 5nr16 . . . . . . . . . . . . . sah

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 cF
K
4
0
L
1
6
2
S
1
6
5
S
1
6
8
H
1
7
2
E
2
6
4
L
2
6
7
E
2
6
8
G
2
7
0
V
2
7
1
L
3
4
3
L
3
4
4
P
3
4
5
P
3
5
0
R
3
5
1
R
3
5
2
L
3
5
3
[1]4qpp.b - . . . . * . . . . . . . . . . .
[1]4y2h.b . . . . . . * . . . . . . . . . . sah
[1]4y30.b . . . . . . * Q . . . . . . . . . sah
[1]5egs.c . . . . . . . . . . . . . . . . . sah

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
4qpp.b:36s
4y2h.b is apo
4y30.b is apo
5egs.c:5nr
[1] 4qpp.b
0
- - 1.5
[1] 4y2h.b 0.4
-
- 1.0
[1] 4y30.b 0.9 -
-
0.9
[1] 5egs.c 0.6 - -
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
4qpp.b
4y2h.b
4y30.b
5egs.c
[1] 4qpp.b
0
.13 .14 .11
[1] 4y2h.b .13
0
.02 .07
[1] 4y30.b .14 .02
0
.08
[1] 5egs.c .11 .07 .08
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 1.1 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
4qpp.b
4y2h.b
4y30.b
5egs.c
[1] 4qpp.b
0
1.1 1.1 1.2
[1] 4y2h.b 1.1
0
0.1 0.8
[1] 4y30.b 1.1 0.1
0
0.9
[1] 5egs.c 1.2 0.8 0.9
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 0.8 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
4qpp.b
4y2h.b
4y30.b
5egs.c
[1] 4qpp.b
0
1.8 1.7 1.9
[1] 4y2h.b 1.8
0
0.6 1.0
[1] 4y30.b 1.7 0.6
0
1.1
[1] 5egs.c 1.9 1.0 1.1
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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