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.

NCSB1_STRCZ_1_332

2,7-dihydroxy-5-methyl-1-naphthoate 7-O-methyltransferase [Class I-like SAM-binding methyltransferase superfamily. Cation-independent O- methyltransferase family]

Composition of the binding site

Protein chains monomer [domain annotation]
A1 (NCSB1_STRCZ):R: S-adenosyl-L-methionine binding (243)
96, 103, 132, 146, 150, 153, 246, 247, 286, 289, 290, 293, 294
96, 103, 132, 146, 150, 153, 243, 246, 247, 286, 289, 290, 293, 294
Cofactors (cF):sah

Full PDB list

3i53, 3i58, 3i5u, 3i64

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1 cF
W
9
6
V
1
0
3
F
1
3
2
F
1
4
6
M
1
5
0
H
1
5
3
A
2
4
3
H
2
4
6
D
2
4
7
M
2
8
6
R
2
8
9
M
2
9
0
Y
2
9
3
F
2
9
4
[1]3i53.a none . . . . . . . . . . . . . . sah
[1]3i58.a 7na17 . . . . . . . . . . . . . . sah
[1]3i5u.a 5na15 . . . . . . . . . . . . . .
[1]3i64.b dna15 . . . . . . . . . . . . . . sah

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 cF
W
9
6
V
1
0
3
F
1
3
2
F
1
4
6
M
1
5
0
H
1
5
3
A
2
4
3
H
2
4
6
D
2
4
7
M
2
8
6
R
2
8
9
M
2
9
0
Y
2
9
3
F
2
9
4
[1]3i53.a . . . . . . . . . . . . . . sah
[1]3i58.a . . . . . . . . . . . . . . sah
[1]3i5u.a . . . . . . . . . . . . . .
[1]3i64.b . . . . . . . . . . . . . . sah

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
3i53.a is apo
3i58.a:7na
3i5u.a:5na
3i64.b:dna
[1] 3i53.a
-
0.1 0 0.1
[1] 3i58.a -
0
0.1 0.2
[1] 3i5u.a - 0.2
0
0.2
[1] 3i64.b - 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
3i53.a
3i58.a
3i5u.a
3i64.b
[1] 3i53.a
0
.01 .01 .01
[1] 3i58.a .01
0
.03 .02
[1] 3i5u.a .01 .03
0
.02
[1] 3i64.b .01 .02 .02
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
3i53.a
3i58.a
3i5u.a
3i64.b
[1] 3i53.a
0
0.5 0.5 0.4
[1] 3i58.a 0.5
0
0.1 0.2
[1] 3i5u.a 0.5 0.1
0
0.2
[1] 3i64.b 0.4 0.2 0.2
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
3i53.a
3i58.a
3i5u.a
3i64.b
[1] 3i53.a
0
1.0 1.0 0.9
[1] 3i58.a 1.0
0
0.4 0.5
[1] 3i5u.a 1.0 0.4
0
0.5
[1] 3i64.b 0.9 0.5 0.5
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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

loading...