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RDMB_STREF_6_374

Aclacinomycin 10-hydroxylase RdmB [Class I-like SAM-binding methyltransferase superfamily. Cation-independent O- methyltransferase family]

Composition of the binding site

Protein chains monomer [domain annotation]
A1 (RDMB_STREF):R: S-adenosyl-L-methionine binding (240, 241)
146, 159, 163, 171, 188, 190:192, 194:197, 213, 214, 217, 239, 242, 255:257, 260, 261
146, 159, 163, 171, 188, 190:192, 194:197, 213, 214, 217, 239:242, 255:257, 260, 261

Full PDB list

1qzz, 1r00, 1xds, 1xdu

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1
W
1
4
6
M
1
6
3
Y
1
7
1
D
1
8
8
G
1
9
0
G
1
9
1
G
1
9
2
G
1
9
4
G
1
9
5
M
1
9
6
L
1
9
7
E
2
1
3
L
2
1
4
P
2
1
7
G
2
3
9
D
2
4
0
F
2
4
1
F
2
4
2
S
2
5
5
F
2
5
6
N
2
6
0
W
2
6
1
[1]1qzz.a sam27 . . . . . . . . . . . . . . . . . . . . . .
[1]1r00.a act-sah30 . . . . . . . . . . . . . . . . . . . . . .
[1]1xds.a sam27 . * - . . . . . . * . . . . . . . . . . . .
[1]1xdu.a sfg27 . * . . . . . . . * . . . . . . . . . . . .

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
4
6
F
1
5
9
M
1
6
3
Y
1
7
1
D
1
8
8
G
1
9
0
G
1
9
1
G
1
9
2
G
1
9
4
G
1
9
5
M
1
9
6
L
1
9
7
E
2
1
3
L
2
1
4
P
2
1
7
G
2
3
9
D
2
4
0
F
2
4
1
F
2
4
2
S
2
5
5
F
2
5
6
V
2
5
7
N
2
6
0
W
2
6
1
[1]1qzz.a . . . . . . . . . . . . . . . . . . . . . . . .
[1]1r00.a . . . . . . . . . . . . . . . . . . . . . . . .
[1]1xds.a . . * - . . . . . . * . . . . . . . . . . . . .
[1]1xdu.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
1qzz.a:sam
1r00.a:act-sah
1xds.a:sam
1xdu.a:sfg
[1] 1qzz.a
0
0.1 0.2 0.1
[1] 1r00.a 0
0
0.4 0.3
[1] 1xds.a 0.3 0.8
0.2
0.2
[1] 1xdu.a 0.1 0.3 0.6
0.2
[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
1qzz.a
1r00.a
1xds.a
1xdu.a
[1] 1qzz.a
0
.02 .03 .02
[1] 1r00.a .02
0
.04 .02
[1] 1xds.a .03 .04
0
.04
[1] 1xdu.a .02 .02 .04
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 0.3 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
1qzz.a
1r00.a
1xds.a
1xdu.a
[1] 1qzz.a
0
0.2 1.5 0.2
[1] 1r00.a 0.2
0
1.5 0.2
[1] 1xds.a 1.5 1.5
0
1.5
[1] 1xdu.a 0.2 0.2 1.5
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
1qzz.a
1r00.a
1xds.a
1xdu.a
[1] 1qzz.a
0
0.2 1.5 0.2
[1] 1r00.a 0.2
0
1.5 0.3
[1] 1xds.a 1.5 1.5
0
1.6
[1] 1xdu.a 0.2 0.3 1.6
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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