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CDLS_BACLD_1_249

Cyclo(L-leucyl-L-leucyl) synthase [CDPS family]

Composition of the binding site

Protein chains monomer [domain annotation]
A1 (CDLS_BACLD):R: Substrate binding (180, 184)
35:37, 65:67, 150, 153, 154, 188, 204, 206
35:37, 65:67, 150, 153, 154, 180, 184, 188, 204, 206

Full PDB list

3oqh, 3oqi, 3oqj, 3s7t (redundant Pocketome entry)

Pocket contact map

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PDB.ch
   
ligand
A1
G
3
5
I
3
6
L
6
5
M
1
5
0
A
1
5
3
A
1
5
4
Y
1
8
0
E
1
8
4
F
1
8
8
Y
2
0
4
R
2
0
6
[1]3oqi.a none . . . . . . . . . . .
[1]3oqj.b 3cx15 . . . . . . . . . . .
[1]3s7t.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

[download in TSV format]
   
PDB.ch
A1
G
3
5
I
3
6
S
3
7
L
6
5
L
6
6
A
6
7
M
1
5
0
A
1
5
3
A
1
5
4
Y
1
8
0
E
1
8
4
F
1
8
8
Y
2
0
4
R
2
0
6
[1]3oqi.a . . . . . . . . . . . . . .
[1]3oqj.b . . . . . . . . . . . . . .
[1]3s7t.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
3oqi.a is apo
3oqj.b:3cx
3s7t.b is apo
[1] 3oqi.a
-
0.1 -
[1] 3oqj.b -
0
-
[1] 3s7t.b - 0.1
-
[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
3oqi.a
3oqj.b
3s7t.b
[1] 3oqi.a
0
.01 .01
[1] 3oqj.b .01
0
.01
[1] 3s7t.b .01 .01
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

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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
3oqi.a
3oqj.b
3s7t.b
[1] 3oqi.a
0
0.4 0.4
[1] 3oqj.b 0.4
0
0.3
[1] 3s7t.b 0.4 0.3
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 0.3 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
3oqi.a
3oqj.b
3s7t.b
[1] 3oqi.a
0
0.6 0.8
[1] 3oqj.b 0.6
0
0.5
[1] 3s7t.b 0.8 0.5
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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