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DCS1_GOSAR_1_554

(+)-delta-cadinene synthase isozyme XC1 [Terpene synthase family]

Composition of the binding site

Protein chains monomer
A1 (DCS1_GOSAR):275, 279, 307, 448, 451, 454, 455, 526, 527, 529:532, 535, 536, 540275, 279, 307, 448, 451, 454, 455, 526, 527, 529:532, 535, 536, 540
Metals (Me):Mg

Full PDB list

3g4d, 3g4f

Pocket contact map

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PDB.ch
   
ligand
A1 Me
E
2
7
5
W
2
7
9
D
3
0
7
R
4
4
8
D
4
5
1
E
4
5
5
L
5
2
6
Y
5
2
7
E
5
2
9
Y
5
3
5
V
5
3
6
A
5
4
0
[1]3g4f.b fpf25 . . . . . . . . . . . . Mg
[2]3g4d.b none . . . . . . . . . - - .

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

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PDB.ch
A1 Me
E
2
7
5
W
2
7
9
D
3
0
7
R
4
4
8
D
4
5
1
A
4
5
4
E
4
5
5
L
5
2
6
Y
5
2
7
E
5
2
9
G
5
3
0
D
5
3
1
G
5
3
2
Y
5
3
5
V
5
3
6
A
5
4
0
[1]3g4f.b . . . . . . . . . . - - - . . . Mg
[2]3g4d.b . . . . . . . . . . * * * - - .

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
3g4f.b:fpf
3g4d.b is apo
[1] 3g4f.b
0.2
-
[2] 3g4d.b 7.9
-
[Pocket-ligand steric clashes matrix]

Pocket clash dissimilarity (2 clusters)

Pockets (x) vs pockets (y) colored by ligand clash profile difference

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pocketpocket
≥1.
.9
.8
.7
.6
.5
.4
.3
.2
.1
.0
3g4f.b
3g4d.b
[1] 3g4f.b
0
.46
[2] 3g4d.b .46
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 0.4 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
3g4f.b
3g4d.b
[1] 3g4f.b
0
0.5
[2] 3g4d.b 0.5
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

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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
3g4f.b
3g4d.b
[1] 3g4f.b
0
0.7
[2] 3g4d.b 0.7
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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