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EGTD_MYCS2_1_321

Histidine N-alpha-methyltransferase [Methyltransferase superfamily. EgtD family]

Composition of the binding site

Protein chains monomer [domain annotation]
A1 (EGTD_MYCS2):R: S-adenosyl-L-methionine binding (141, 142)
R: L-histidine binding (282, 284)
36, 38, 39, 47, 50, 56, 59, 86:89, 92, 112:115, 140, 143, 160:163, 166, 206, 213, 216, 252
36, 38, 39, 47, 50, 56, 59, 86:89, 92, 112:115, 140:143, 160:163, 166, 206, 213, 216, 252, 282, 284

Full PDB list

4pim, 4pin, 4pio, 4pip, 4uy5, 4uy6, 4uy7 (redundant Pocketome entry)

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1
K
3
6
Y
3
9
F
4
7
Y
5
6
G
8
6
S
8
7
G
8
8
K
9
2
F
1
1
2
D
1
1
3
V
1
1
4
G
1
4
0
D
1
4
1
F
1
4
2
G
1
6
1
S
1
6
2
T
1
6
3
N
1
6
6
Y
2
0
6
T
2
1
3
F
2
1
6
M
2
5
2
E
2
8
2
S
2
8
4
[1]4pin.a avi13 . . . . . . - . . . . . . . . . . . . . . . . .
[1]4pio.a avi,sah39 . . . . . . . . . . . . . . . . . . . . . . . .
[1]4pip.c Wsah41 . . . . . . . . . . . . . . . . . . . . . V A .
[1]4uy5.a none . . . . . . . . . . . . . . . . . . . . . * . .
[1]4uy6.a Hsah37 . . . . . . . . . . . . . . . . . . . . . . . .
[1]4uy7.a H11 . . . . . . . . . . . . . . . . . . . . . . . .

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
K
3
6
F
3
8
Y
3
9
F
4
7
I
5
0
Y
5
6
T
5
9
G
8
6
S
8
7
G
8
8
T
8
9
K
9
2
F
1
1
2
D
1
1
3
V
1
1
4
D
1
1
5
G
1
4
0
D
1
4
1
F
1
4
2
E
1
4
3
L
1
6
0
G
1
6
1
S
1
6
2
T
1
6
3
N
1
6
6
Y
2
0
6
T
2
1
3
F
2
1
6
M
2
5
2
E
2
8
2
S
2
8
4
[1]4pin.a . . . . . . . . . - - . . . . . . . . . . . . . . . . . . * .
[1]4pio.a . . . . . . . . . . . . . . . . . . . . . . . . . . . . . * .
[1]4pip.c . . . . . . . . . . . . . . . . . . . . . . . . . . . . V A .
[1]4uy5.a . . . . . . . . . . . . . . . . . . . . . . . . . . . . * * .
[1]4uy6.a . . . . . . . . . . . . . . . . . . . . . . . . . . . . . * .
[1]4uy7.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
4pin.a:avi
4pio.a:avi,sah
4pip.c:Wsah
4uy5.a is apo
4uy6.a:Hsah
4uy7.a:H
[1] 4pin.a
0.1
0.8 2.1 - 0.4 0.2
[1] 4pio.a 0.1
0
1.8 - 0.2 0
[1] 4pip.c 0.1 0.2
0
- 0.5 0
[1] 4uy5.a 0.3 1.3 2.8
-
1.0 0.3
[1] 4uy6.a 0.3 0.4 1.7 -
0.1
0.2
[1] 4uy7.a 0.2 0.8 2.7 - 0.8
0.3
[Pocket-ligand steric clashes matrix]

Pocket clash dissimilarity (1 cluster)

Pockets (x) vs pockets (y) colored by ligand clash profile difference

zoom: [−] [+]; [view as image]; [download as text]

pocketpocket
≥1.
.9
.8
.7
.6
.5
.4
.3
.2
.1
.0
4pin.a
4pio.a
4pip.c
4uy5.a
4uy6.a
4uy7.a
[1] 4pin.a
0
.03 .08 .06 .03 .05
[1] 4pio.a .03
0
.08 .06 .02 .05
[1] 4pip.c .08 .08
0
.12 .07 .11
[1] 4uy5.a .06 .06 .12
0
.05 .03
[1] 4uy6.a .03 .02 .07 .05
0
.04
[1] 4uy7.a .05 .05 .11 .03 .04
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 1.5 Å)

Pockets (x) vs pockets (y) colored by RMSD of site residue backbone 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
4pin.a
4pio.a
4pip.c
4uy5.a
4uy6.a
4uy7.a
[1] 4pin.a
0
1.4 1.4 1.9 1.4 1.5
[1] 4pio.a 1.4
0
0.2 2.2 0.2 2.0
[1] 4pip.c 1.4 0.2
0
2.2 0.3 2.0
[1] 4uy5.a 1.9 2.2 2.2
0
2.1 0.7
[1] 4uy6.a 1.4 0.2 0.3 2.1
0
1.9
[1] 4uy7.a 1.5 2.0 2.0 0.7 1.9
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 1.4 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
4pin.a
4pio.a
4pip.c
4uy5.a
4uy6.a
4uy7.a
[1] 4pin.a
0
1.4 1.5 1.9 1.4 1.5
[1] 4pio.a 1.4
0
0.5 2.4 0.4 2.2
[1] 4pip.c 1.5 0.5
0
2.5 0.6 2.2
[1] 4uy5.a 1.9 2.4 2.5
0
2.3 1.1
[1] 4uy6.a 1.4 0.4 0.6 2.3
0
2.1
[1] 4uy7.a 1.5 2.2 2.2 1.1 2.1
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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