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GNMT_HUMAN_2_295

Glycine N-methyltransferase [Class I-like SAM-binding methyltransferase superfamily. Glycine N-methyltransferase family]

Composition of the binding site

Protein chains homodimer
A1 (GNMT_HUMAN):149, 208, 210, 217, 218, 220, 242149, 208, 210, 217, 218, 220, 242
A2 (GNMT_HUMAN):149, 208, 210, 217, 218, 220, 242149, 208, 210, 217, 218, 220, 242

Full PDB list

1bhj, 1d2c, 1d2g, 1d2h, 1kia, 1nbh, 1nbi, 1r74, 1xva, 2azt, 2idj, 2idk, 3thr, 3ths (redundant Pocketome entry)

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1 A2
L
2
1
0
H
2
1
7
M
2
1
8
C
1
4
9
L
2
1
0
H
2
1
7
M
2
1
8
T
2
2
0
R
2
4
2
[1]1d2c.b none . . . S . . . . .
[1]1kia.c none . . . - - - - - -
[1]1r74.a none . . . . . . . . .
[1]3thr.a c2f33 . . . S . . . . .
[1]3ths.a 03o.ggl.ggl33 . . . S . . . . .

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 A2
C
1
4
9
S
2
0
8
L
2
1
0
H
2
1
7
M
2
1
8
T
2
2
0
R
2
4
2
C
1
4
9
S
2
0
8
L
2
1
0
H
2
1
7
M
2
1
8
T
2
2
0
R
2
4
2
[1]1d2c.b S . . . . . . S . . . . . .
[1]1kia.c S . . . . . . - - - - - - -
[1]1r74.a . . . . . . . . . . . . . .
[1]3thr.a S . . . . . . S . . . . . .
[1]3ths.a S . . . . . . S . . . . . .

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
1d2c.b is apo
1kia.c is apo
1r74.a is apo
3thr.a:c2f
3ths.a:03o.ggl.ggl
[1] 1d2c.b
-
- - 0.4 0.2
[1] 1kia.c -
-
- 0.3 0
[1] 1r74.a - -
-
0.3 0.5
[1] 3thr.a - - -
0
0.1
[1] 3ths.a - - - 0.1
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
1d2c.b
1kia.c
1r74.a
3thr.a
3ths.a
[1] 1d2c.b
0
.02 .03 .03 .02
[1] 1kia.c .02
0
.04 .03 .01
[1] 1r74.a .03 .04
0
.04 .04
[1] 3thr.a .03 .03 .04
0
.01
[1] 3ths.a .02 .01 .04 .01
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
1d2c.b
1kia.c
1r74.a
3thr.a
3ths.a
[1] 1d2c.b
0
0.3 0.7 0.5 0.5
[1] 1kia.c 0.3
0
0.5 0.3 0.4
[1] 1r74.a 0.7 0.5
0
0.4 0.5
[1] 3thr.a 0.5 0.3 0.4
0
0.3
[1] 3ths.a 0.5 0.4 0.5 0.3
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 0.4 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
1d2c.b
1kia.c
1r74.a
3thr.a
3ths.a
[1] 1d2c.b
0
0.5 0.9 0.7 0.8
[1] 1kia.c 0.5
0
0.7 0.7 0.7
[1] 1r74.a 0.9 0.7
0
0.7 0.8
[1] 3thr.a 0.7 0.7 0.7
0
0.5
[1] 3ths.a 0.8 0.7 0.8 0.5
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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