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ANM5_HUMAN_2_637

Protein arginine N-methyltransferase 5 [Class I-like SAM-binding methyltransferase superfamily. Protein arginine N- methyltransferase family]

Composition of the binding site

Protein chains monomer [domain annotation]
A1 (ANM5_HUMAN):D: SAM-dependent MTase PRMT-type (308:313, 319, 323, 324, 326, 327, 333, 435, 437:439, 444, 503, 577:580)
R: S-adenosyl-L-methionine binding (333)
R: Beta barrel (503, 577:580)
300, 301, 304, 307
300, 301, 304, 307:313, 319, 323, 324, 326, 327, 333, 435, 437:439, 444, 503, 577:580
Cofactors (cF):0xu/mta/sam/sfg

Full PDB list

4gqb, 4x60, 4x61, 4x63, 5c9z, 5emj, 5emk, 5eml, 5emm, 5fa5 (redundant Pocketome entry)

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1 cF
F
3
0
0
Y
3
0
4
Y
3
0
7
L
3
0
8
Q
3
0
9
S
3
1
0
P
3
1
1
L
3
1
2
L
3
1
9
T
3
2
3
Y
3
2
4
V
3
2
6
F
3
2
7
K
3
3
3
E
4
3
5
L
4
3
7
G
4
3
8
S
4
3
9
E
4
4
4
V
5
0
3
F
5
7
7
S
5
7
8
W
5
7
9
F
5
8
0
[1]4gqb.a aceSGRGKGGK54 . . . . . . . . . . . . . . . . . . . . . . . . 0xu
[1]4x60.a 3xv28 . . . . . . . . . . . . . . . . . . . . . . . . sfg
[1]5c9z.a 4z228 . . . . . . . . . . . . . . . . . . . . . . . . sfg
[1]5emj.a 5qj31 . . . . . . . . . . . . . . . . . . . . . . . . sfg
[1]5emk.a 5qh29 . . . . . . . . . . . . . . . . . . . . . . . . sfg
[1]5eml.a 5qk29 . . . . . . . . . . . . . . . . . . . . . . . . sam
[1]5emm.a 5ql30 . . . . . . . . . . . . . . . . . . . . . . . . sfg
[1]5fa5.a R11 . . . . . . . . . . . . . . . . . . . . . . . . mta

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 cF
F
3
0
0
A
3
0
1
Y
3
0
4
Y
3
0
7
L
3
0
8
Q
3
0
9
S
3
1
0
P
3
1
1
L
3
1
2
Q
3
1
3
L
3
1
9
T
3
2
3
Y
3
2
4
V
3
2
6
F
3
2
7
K
3
3
3
E
4
3
5
L
4
3
7
G
4
3
8
S
4
3
9
E
4
4
4
V
5
0
3
F
5
7
7
S
5
7
8
W
5
7
9
F
5
8
0
[1]4gqb.a * . . . . . . . . . . . . . * . . . . . . . . . . . 0xu
[1]4x60.a . . . . . . . . . . . . . . . . . . . . . . . . . . sfg
[1]5c9z.a . . . . . . . . . . . . . . . . . . . . . . . . . . sfg
[1]5emj.a * . . . . . . . . . . . . . . . . . . . . . . . . . sfg
[1]5emk.a * . . . . . . . . . . . . . . . . . . . . . . . . . sfg
[1]5eml.a * . . . . * . . . . . . . . . . . . . . . . . . . . sam
[1]5emm.a . . . . . . . . . . . . . . . . . . . . . . . . . . sfg
[1]5fa5.a * . . . . . . . . . . . . . * . . . . . . . . . . . mta

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
4gqb.a:aceSGRGKGGK
4x60.a:3xv
5c9z.a:4z2
5emj.a:5qj
5emk.a:5qh
5eml.a:5qk
5emm.a:5ql
5fa5.a:R
[1] 4gqb.a
0
5.6 5.7 4.0 4.0 3.6 6.8 0
[1] 4x60.a 0.9
0
0.1 0.9 0.4 0.3 0.3 0
[1] 5c9z.a 0.6 0
0
0.6 0.8 0.3 0.3 0
[1] 5emj.a 0.4 2.9 3.1
0.1
0.3 0 3.9 0
[1] 5emk.a 0.2 2.3 2.5 0.1
0
0 3.7 0
[1] 5eml.a 0.3 2.6 2.8 0.1 0.7
0
3.9 0
[1] 5emm.a 0.7 0 0 0.7 0.7 0.3
0
0
[1] 5fa5.a 0.2 6.0 6.2 3.9 3.8 3.8 7.0
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
4gqb.a
4x60.a
5c9z.a
5emj.a
5emk.a
5eml.a
5emm.a
5fa5.a
[1] 4gqb.a
0
.31 .29 .19 .18 .20 .32 .03
[1] 4x60.a .31
0
.05 .20 .19 .21 .05 .31
[1] 5c9z.a .29 .05
0
.17 .17 .17 .05 .29
[1] 5emj.a .19 .20 .17
0
.02 .02 .20 .17
[1] 5emk.a .18 .19 .17 .02
0
.03 .20 .16
[1] 5eml.a .20 .21 .17 .02 .03
0
.20 .18
[1] 5emm.a .32 .05 .05 .20 .20 .20
0
.32
[1] 5fa5.a .03 .31 .29 .17 .16 .18 .32
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 1.0 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
4gqb.a
4x60.a
5c9z.a
5emj.a
5emk.a
5eml.a
5emm.a
5fa5.a
[1] 4gqb.a
0
1.1 1.0 0.7 0.4 0.4 0.9 0.2
[1] 4x60.a 1.1
0
0.2 0.6 0.9 1.0 0.6 1.1
[1] 5c9z.a 1.0 0.2
0
0.5 0.8 0.9 0.5 1.0
[1] 5emj.a 0.7 0.6 0.5
0
0.4 0.5 0.4 0.7
[1] 5emk.a 0.4 0.9 0.8 0.4
0
0.2 0.6 0.5
[1] 5eml.a 0.4 1.0 0.9 0.5 0.2
0
0.8 0.4
[1] 5emm.a 0.9 0.6 0.5 0.4 0.6 0.8
0
0.9
[1] 5fa5.a 0.2 1.1 1.0 0.7 0.5 0.4 0.9
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 0.6 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
4gqb.a
4x60.a
5c9z.a
5emj.a
5emk.a
5eml.a
5emm.a
5fa5.a
[1] 4gqb.a
0
1.6 1.5 1.1 1.0 0.9 1.3 0.8
[1] 4x60.a 1.6
0
0.6 1.1 1.2 1.3 0.8 1.6
[1] 5c9z.a 1.5 0.6
0
1.1 1.2 1.3 0.7 1.6
[1] 5emj.a 1.1 1.1 1.1
0
0.6 0.6 0.6 1.2
[1] 5emk.a 1.0 1.2 1.2 0.6
0
0.4 0.8 1.1
[1] 5eml.a 0.9 1.3 1.3 0.6 0.4
0
0.9 1.1
[1] 5emm.a 1.3 0.8 0.7 0.6 0.8 0.9
0
1.3
[1] 5fa5.a 0.8 1.6 1.6 1.2 1.1 1.1 1.3
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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