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CYC2_STRCO_1_338

Germacradienol/geosmin synthase [Terpene synthase family]

Composition of the binding site

Protein chains monomer [domain annotation]
A1 (CYC2_STRCO):R: Germacradienol/germacrene D synthase (82, 83, 86, 184, 229, 233, 236, 237, 325, 326)82, 83, 86, 184, 229, 233, 236, 237, 325, 326
Metals (Me):Mg

Full PDB list

5dw7, 5dz2

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1 Me
V
8
2
F
8
3
D
8
6
R
1
8
4
N
2
2
9
S
2
3
3
R
2
3
6
E
2
3
7
R
3
2
5
Y
3
2
6
[1]5dw7.a none . . . . . . . . . .
[1]5dz2.a 21214 . . . . . . . . . . Mg

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 Me
V
8
2
F
8
3
D
8
6
R
1
8
4
N
2
2
9
S
2
3
3
R
2
3
6
E
2
3
7
R
3
2
5
Y
3
2
6
[1]5dw7.a . . . . . . . . . .
[1]5dz2.a . . . . . . . . . . Mg

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
5dw7.a is apo
5dz2.a:212
[1] 5dw7.a
-
0.1
[1] 5dz2.a -
0
[Pocket-ligand steric clashes matrix]

Pocket clash dissimilarity (1 cluster)

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
5dw7.a
5dz2.a
[1] 5dw7.a
0
.01
[1] 5dz2.a .01
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 2.9 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
5dw7.a
5dz2.a
[1] 5dw7.a
0
2.6
[1] 5dz2.a 2.6
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 1.3 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
5dw7.a
5dz2.a
[1] 5dw7.a
0
5.7
[1] 5dz2.a 5.7
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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