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.

SILD_PODPE_1_278

Secoisolariciresinol dehydrogenase [Short-chain dehydrogenases/reductases (SDR) family]

Composition of the binding site

Protein chains monomer
A1 (SILD_PODPE):23, 25:28, 47, 48, 71:74, 99:102, 124, 151:153, 167, 171, 197:20023, 25:28, 47, 48, 71:74, 99:102, 124, 151:153, 167, 171, 197:200

Full PDB list

2bgk, 2bgl, 2bgm (redundant Pocketome entry)

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1
G
2
3
G
2
6
G
2
7
I
2
8
D
4
7
I
4
8
C
7
1
D
7
2
V
7
3
N
9
9
G
1
0
1
V
1
0
2
I
1
2
4
T
1
5
1
A
1
5
2
S
1
5
3
Y
1
6
7
K
1
7
1
P
1
9
7
Y
1
9
8
I
1
9
9
V
2
0
0
[1]2bgk.a none . . . . . . . . . . . . . . . . . . . . . .
[1]2bgl.a naj44 . . . . . . . . . . . . . . . . . . . . . .

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
G
2
3
A
2
5
G
2
6
G
2
7
I
2
8
D
4
7
I
4
8
C
7
1
D
7
2
V
7
3
T
7
4
N
9
9
V
1
0
0
G
1
0
1
V
1
0
2
I
1
2
4
T
1
5
1
A
1
5
2
S
1
5
3
Y
1
6
7
K
1
7
1
P
1
9
7
Y
1
9
8
I
1
9
9
V
2
0
0
[1]2bgk.a . . . . . . . . . . . . . . . . . . . . . . . . .
[1]2bgl.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
2bgk.a is apo
2bgl.a:naj
[1] 2bgk.a
-
0.5
[1] 2bgl.a -
0.1
[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
2bgk.a
2bgl.a
[1] 2bgk.a
0
.02
[1] 2bgl.a .02
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 0.6 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
2bgk.a
2bgl.a
[1] 2bgk.a
0
0.9
[1] 2bgl.a 0.9
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 0.5 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
2bgk.a
2bgl.a
[1] 2bgk.a
0
1.1
[1] 2bgl.a 1.1
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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

loading...