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DNRK_STRPE_3_355

Carminomycin 4-O-methyltransferase DnrK [Class I-like SAM-binding methyltransferase superfamily. Cation-independent O- methyltransferase family]

Composition of the binding site

Protein chains monomer [domain annotation]
A1 (DNRK_STRPE):R: S-adenosyl-L-methionine binding (237, 238)
106, 113, 142, 143, 153, 156, 159:163, 166:168, 187:189, 210, 211, 236, 239, 252:254, 256:258, 283, 297, 299, 300, 303, 304, 307, 308, 337, 339, 340, 342, 344
106, 113, 142, 143, 153, 156, 159:163, 166:168, 187:189, 210, 211, 236:239, 252:254, 256:258, 283, 297, 299, 300, 303, 304, 307, 308, 337, 339, 340, 342, 344

Full PDB list

1tw2, 1tw3, 4wxh, 5eeg, 5eeh, 5jr3 (redundant Pocketome entry)

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1
W
1
0
6
V
1
1
3
F
1
4
2
Y
1
4
3
R
1
5
3
F
1
5
6
L
1
6
0
C
1
6
2
D
1
6
3
V
1
6
6
A
1
6
7
F
1
6
8
G
1
8
7
G
1
8
8
G
1
8
9
E
2
1
0
M
2
1
1
G
2
3
6
D
2
3
7
F
2
3
8
F
2
3
9
S
2
5
2
F
2
5
3
N
2
5
7
W
2
5
8
E
2
9
9
L
3
0
0
R
3
0
3
M
3
0
4
F
3
0
7
L
3
0
8
I
3
4
0
Y
3
4
2
[1]1tw3.a ert,sah69 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]4wxh.b 3vl,sah67 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]5eeg.a s8m28 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . - .
[1]5eeh.a p9p,p9p,p9p,sah59 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]5jr3.c 4mu,sah39 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

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
W
1
0
6
V
1
1
3
F
1
4
2
Y
1
4
3
R
1
5
3
F
1
5
6
L
1
5
9
L
1
6
0
A
1
6
1
C
1
6
2
D
1
6
3
V
1
6
6
A
1
6
7
F
1
6
8
G
1
8
7
G
1
8
8
G
1
8
9
E
2
1
0
M
2
1
1
G
2
3
6
D
2
3
7
F
2
3
8
F
2
3
9
S
2
5
2
F
2
5
3
V
2
5
4
L
2
5
6
N
2
5
7
W
2
5
8
H
2
8
3
F
2
9
7
E
2
9
9
L
3
0
0
R
3
0
3
M
3
0
4
F
3
0
7
L
3
0
8
S
3
3
7
T
3
3
9
I
3
4
0
Y
3
4
2
L
3
4
4
[1]1tw3.a . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]4wxh.b . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]5eeg.a . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . * . . . . . - - - . .
[1]5eeh.a . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . * . . . . . . . . . .
[1]5jr3.c . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

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
1tw3.a:ert,sah
4wxh.b:3vl,sah
5eeg.a:s8m
5eeh.a:p9p,sah
5jr3.c:4mu,sah
[1] 1tw3.a
0.1
0.4 0.1 1.4 0.4
[1] 4wxh.b 0.5
0
0 0.2 0.2
[1] 5eeg.a 2.6 2.7
0
1.0 0.5
[1] 5eeh.a 2.3 1.5 0.1
0
0.3
[1] 5jr3.c 1.4 1.0 0 0.9
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
1tw3.a
4wxh.b
5eeg.a
5eeh.a
5jr3.c
[1] 1tw3.a
0
.04 .09 .09 .06
[1] 4wxh.b .04
0
.08 .05 .04
[1] 5eeg.a .09 .08
0
.07 .05
[1] 5eeh.a .09 .05 .07
0
.06
[1] 5jr3.c .06 .04 .05 .06
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

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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
1tw3.a
4wxh.b
5eeg.a
5eeh.a
5jr3.c
[1] 1tw3.a
0
0.9 0.5 1.8 0.9
[1] 4wxh.b 0.9
0
0.8 1.8 0.9
[1] 5eeg.a 0.5 0.8
0
1.5 0.4
[1] 5eeh.a 1.8 1.8 1.5
0
1.4
[1] 5jr3.c 0.9 0.9 0.4 1.4
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 0.9 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
1tw3.a
4wxh.b
5eeg.a
5eeh.a
5jr3.c
[1] 1tw3.a
0
2.1 0.7 1.9 1.2
[1] 4wxh.b 2.1
0
2.0 2.5 1.9
[1] 5eeg.a 0.7 2.0
0
1.6 0.8
[1] 5eeh.a 1.9 2.5 1.6
0
1.5
[1] 5jr3.c 1.2 1.9 0.8 1.5
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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