If you see this message after the page is completely loaded, then JavaScript is not supported or disabled in your browser. Please consider enabling JavaScript for this site.

MCE_VACCW_1_302

Cap-specific mRNA (nucleoside-2'-O-)-methyltransferase [Class I-like SAM-binding methyltransferase superfamily. Poxvirus/kinetoplastid 2'-O-MTase family]

Composition of the binding site

Protein chains monomer [domain annotation]
A1 (MCE_VACCW):R: Binding to NPH-I (177, 180, 182, 202, 204, 205, 207, 233)
R: Binding to Rap94 (182, 202, 204, 233)
R: mRNA cap binding (177, 180)
R: mRNA cap binding (205, 207)
22, 24, 27, 146:148
22, 24, 27, 146:148, 177, 180, 182, 202, 204, 205, 207, 233

Full PDB list

1av6, 1b42, 1bky, 1eam, 1eqa, 1jsz, 1jte, 1jtf, 1p39, 1v39, 1vp3, 1vp9, 1vpt, 2ga9, 2gaf, 2vp3, 3er8, 3er9, 3erc, 3mag, 3mct, 4dcg (redundant Pocketome entry)

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1
Y
2
2
P
2
4
A
2
7
P
1
4
8
R
1
7
7
F
1
8
0
D
1
8
2
P
2
0
2
Y
2
0
4
S
2
0
5
E
2
0
7
E
2
3
3
[1]1b42.a m1a11 . . . . . . . . . . . .
[1]1bky.a 1mc9 . . . . . . . . . . . .
[1]1eam.a none . . - . . . . . . . . A
[1]1eqa.a mg721 . . . . . . . . . . . Q
[1]1jsz.a ndm13 . . . . . . . . . . . .
[1]1jte.a none . . . . . W . . . . . .
[1]1jtf.a m7g28 . . . . . W . . . . . .
[1]1p39.a mgt32 . . . . . . . . . . . .
[1]1v39.a m7g29 . . . . . . . . . . . .
[1]3er8.a none . . - . . . . . . . . .
[1]3mag.a 3ma11 . . . . . . . . . . . .
[1]3mct.a 3mc9 . . . . . . . . . . . .
[1]4dcg.a mg721 . . . . . . A . . . . .

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
Y
2
2
P
2
4
A
2
7
N
1
4
6
E
1
4
7
P
1
4
8
R
1
7
7
F
1
8
0
D
1
8
2
P
2
0
2
Y
2
0
4
S
2
0
5
E
2
0
7
E
2
3
3
[1]1b42.a . . . - - . . . . . . . . .
[1]1bky.a . . . - - . . . . . . . . .
[1]1eam.a . . - - - . . . . . . . . A
[1]1eqa.a . . . - - . . . . . . . . Q
[1]1jsz.a . . . - - . . . . . . . . .
[1]1jte.a . . . - - . . W . . . . . .
[1]1jtf.a . . . - - . . W . . . . . .
[1]1p39.a . . . - - . . . . . . . . .
[1]1v39.a . . . - - . . . . . . . . .
[1]3er8.a . . - . . . . . . . . . . .
[1]3mag.a . . . - - . . . . . . . . .
[1]3mct.a . . . - - . . . . . . . . .
[1]4dcg.a . . . - - . . . 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

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

pocketligand
≥10
9
8
7
6
5
4
3
2
1
0
1b42.a:m1a
1bky.a:1mc
1eam.a is apo
1eqa.a:mg7
1jsz.a:ndm
1jte.a is apo
1jtf.a:m7g
1p39.a:mgt
1v39.a:m7g
3er8.a is apo
3mag.a:3ma
3mct.a:3mc
4dcg.a:mg7
[1] 1b42.a
0
0 - 0.1 0.1 - 0 0 0 - 0 0 0
[1] 1bky.a 0.1
0
- 0.1 0 - 0 0 0 - 0 0 0
[1] 1eam.a 0.6 0.8
-
0.7 0.7 - 0.6 0.8 0.8 - 1.1 0.9 0.8
[1] 1eqa.a 0.1 0 -
0.1
0.2 - 0.1 0.1 0.1 - 0.1 0 0.1
[1] 1jsz.a 0.1 0 - 0.1
0
- 0 0 0 - 0.1 0 0
[1] 1jte.a 0.3 0 - 0.1 0.1
-
0 0 0 - 0 0 0
[1] 1jtf.a 0 0 - 0.1 0.1 -
0
0 0 - 0 0 0
[1] 1p39.a 0 0 - 0.1 0 - 0
0
0 - 0.1 0 0
[1] 1v39.a 0 0 - 0.1 0 - 0 0
0
- 0.1 0 0
[1] 3er8.a 0.9 0.5 - 0.6 1.2 - 2.4 2.4 2.3
-
0.4 0.4 0.7
[1] 3mag.a 0.1 0 - 0.1 0.1 - 0 0 0 -
0
0 0
[1] 3mct.a 0 0 - 0.1 0.1 - 0 0 0 - 0.1
0
0
[1] 4dcg.a 0.1 0 - 0.1 0 - 0 0 0 - 0.1 0
0
[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
1b42.a
1bky.a
1eam.a
1eqa.a
1jsz.a
1jte.a
1jtf.a
1p39.a
1v39.a
3er8.a
3mag.a
3mct.a
4dcg.a
[1] 1b42.a
0
.01 .11 .01 .02 .03 0 .01 .01 .20 .01 .01 .02
[1] 1bky.a .01
0
.11 .03 .01 .01 .01 .01 .01 .20 .02 .02 .01
[1] 1eam.a .11 .11
0
.11 .10 .09 .11 .11 .11 .24 .11 .10 .10
[1] 1eqa.a .01 .03 .11
0
.02 .04 .01 .01 .01 .19 .02 .01 .02
[1] 1jsz.a .02 .01 .10 .02
0
.02 .02 .01 .01 .19 .03 .01 0
[1] 1jte.a .03 .01 .09 .04 .02
0
.03 .03 .03 .19 .04 .04 .02
[1] 1jtf.a 0 .01 .11 .01 .02 .03
0
.01 .01 .20 .01 .01 .02
[1] 1p39.a .01 .01 .11 .01 .01 .03 .01
0
0 .20 .02 .01 .01
[1] 1v39.a .01 .01 .11 .01 .01 .03 .01 0
0
.20 .02 .01 .01
[1] 3er8.a .20 .20 .24 .19 .19 .19 .20 .20 .20
0
.19 .19 .19
[1] 3mag.a .01 .02 .11 .02 .03 .04 .01 .02 .02 .19
0
.01 .03
[1] 3mct.a .01 .02 .10 .01 .01 .04 .01 .01 .01 .19 .01
0
.01
[1] 4dcg.a .02 .01 .10 .02 0 .02 .02 .01 .01 .19 .03 .01
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 0.5 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
1b42.a
1bky.a
1eam.a
1eqa.a
1jsz.a
1jte.a
1jtf.a
1p39.a
1v39.a
3er8.a
3mag.a
3mct.a
4dcg.a
[1] 1b42.a
0
0.2 0.2 0.2 0.1 0.2 0.2 0.2 0.3 0.4 0.1 0.1 0.2
[1] 1bky.a 0.2
0
0.2 0.2 0.2 0.2 0.2 0.3 0.3 0.4 0.1 0.2 0.1
[1] 1eam.a 0.2 0.2
0
0.2 0.2 0.2 0.3 0.2 0.4 0.5 0.2 0.2 0.2
[1] 1eqa.a 0.2 0.2 0.2
0
0.2 0.2 0.2 0.2 0.3 0.5 0.2 0.2 0.2
[1] 1jsz.a 0.1 0.2 0.2 0.2
0
0.2 0.2 0.2 0.3 0.4 0.1 0.1 0.1
[1] 1jte.a 0.2 0.2 0.2 0.2 0.2
0
0.2 0.3 0.3 0.4 0.2 0.2 0.2
[1] 1jtf.a 0.2 0.2 0.3 0.2 0.2 0.2
0
0.3 0.3 0.5 0.2 0.2 0.3
[1] 1p39.a 0.2 0.3 0.2 0.2 0.2 0.3 0.3
0
0.4 0.5 0.2 0.2 0.2
[1] 1v39.a 0.3 0.3 0.4 0.3 0.3 0.3 0.3 0.4
0
0.5 0.3 0.3 0.3
[1] 3er8.a 0.4 0.4 0.5 0.5 0.4 0.4 0.5 0.5 0.5
0
0.4 0.5 0.4
[1] 3mag.a 0.1 0.1 0.2 0.2 0.1 0.2 0.2 0.2 0.3 0.4
0
0.1 0.2
[1] 3mct.a 0.1 0.2 0.2 0.2 0.1 0.2 0.2 0.2 0.3 0.5 0.1
0
0.1
[1] 4dcg.a 0.2 0.1 0.2 0.2 0.1 0.2 0.3 0.2 0.3 0.4 0.2 0.1
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

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
1b42.a
1bky.a
1eam.a
1eqa.a
1jsz.a
1jte.a
1jtf.a
1p39.a
1v39.a
3er8.a
3mag.a
3mct.a
4dcg.a
[1] 1b42.a
0
0.2 0.7 0.2 0.5 0.6 0.6 0.5 0.5 0.6 0.2 0.2 0.2
[1] 1bky.a 0.2
0
0.7 0.3 0.5 0.6 0.6 0.5 0.4 0.6 0.2 0.2 0.2
[1] 1eam.a 0.7 0.7
0
0.6 0.7 0.8 0.8 0.7 0.7 0.8 0.6 0.6 0.6
[1] 1eqa.a 0.2 0.3 0.6
0
0.4 0.6 0.6 0.4 0.4 0.6 0.2 0.2 0.3
[1] 1jsz.a 0.5 0.5 0.7 0.4
0
0.4 0.5 0.5 0.5 0.8 0.5 0.5 0.5
[1] 1jte.a 0.6 0.6 0.8 0.6 0.4
0
0.4 0.7 0.6 0.8 0.6 0.6 0.6
[1] 1jtf.a 0.6 0.6 0.8 0.6 0.5 0.4
0
0.7 0.6 0.8 0.6 0.6 0.7
[1] 1p39.a 0.5 0.5 0.7 0.4 0.5 0.7 0.7
0
0.5 0.8 0.5 0.5 0.5
[1] 1v39.a 0.5 0.4 0.7 0.4 0.5 0.6 0.6 0.5
0
0.7 0.4 0.4 0.5
[1] 3er8.a 0.6 0.6 0.8 0.6 0.8 0.8 0.8 0.8 0.7
0
0.6 0.6 0.6
[1] 3mag.a 0.2 0.2 0.6 0.2 0.5 0.6 0.6 0.5 0.4 0.6
0
0.2 0.2
[1] 3mct.a 0.2 0.2 0.6 0.2 0.5 0.6 0.6 0.5 0.4 0.6 0.2
0
0.2
[1] 4dcg.a 0.2 0.2 0.6 0.3 0.5 0.6 0.7 0.5 0.5 0.6 0.2 0.2
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

L C X E | Background Color: | Anaglyph Stereo:

loading...