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ALLN1_ALLSA_39_471

Alliin lyase 1 [Alliinase family]

Composition of the binding site

Protein chains homodimer
A1 (ALLN1_ALLSA):102, 169:171, 203, 241, 245, 263, 265, 266, 286, 288, 289, 297, 401, 426, 439102, 169:171, 203, 241, 245, 263, 265, 266, 286, 288, 289, 297, 401, 426, 439
A2 (ALLN1_ALLSA):130130

Full PDB list

1lk9, 2hor, 2hox

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1 A2
G
1
0
2
G
1
6
9
V
1
7
0
T
1
7
1
Y
2
0
3
T
2
4
1
N
2
4
5
D
2
6
3
V
2
6
5
Y
2
6
6
T
2
8
6
S
2
8
8
K
2
8
9
R
2
9
7
Y
4
0
1
R
4
3
9
Y
1
3
0
[1]1lk9.a plp15 . . . . . . . . . . . . * . . . .
[1]1lk9.b plp-dha21 . . . . . . . . . . . . * . . . .
[1]2hor.a none . . . . . . . . . . . . . . . . -
[1]2hox.a p1t21 . . . . . . . . . . . . . . . . .

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 A2
G
1
0
2
G
1
6
9
V
1
7
0
T
1
7
1
Y
2
0
3
T
2
4
1
N
2
4
5
D
2
6
3
V
2
6
5
Y
2
6
6
T
2
8
6
S
2
8
8
K
2
8
9
R
2
9
7
Y
4
0
1
Q
4
2
6
R
4
3
9
Y
1
3
0
[1]1lk9.a . . . . . . . . . . . . * . . . . .
[1]1lk9.b . . . . . . . . . . . . * . . . . .
[1]2hor.a . . . . . . . . . . . . . . . . . -
[1]2hox.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

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pocketligand
≥10
9
8
7
6
5
4
3
2
1
0
1lk9.a:plp
1lk9.b:plp-dha
2hor.a is apo
2hox.a:p1t
[1] 1lk9.a
0.7
0.5 - 0.4
[1] 1lk9.b 0.7
0.7
- 0.4
[1] 2hor.a 0.1 0.2
-
0.2
[1] 2hox.a 0.1 0.2 -
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
1lk9.a
1lk9.b
2hor.a
2hox.a
[1] 1lk9.a
0
.01 .03 .04
[1] 1lk9.b .01
0
.03 .04
[1] 2hor.a .03 .03
0
.01
[1] 2hox.a .04 .04 .01
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 0.3 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
1lk9.a
1lk9.b
2hor.a
2hox.a
[1] 1lk9.a
0
0.1 0.1 0.1
[1] 1lk9.b 0.1
0
0.1 0.1
[1] 2hor.a 0.1 0.1
0
0.2
[1] 2hox.a 0.1 0.1 0.2
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 0.1 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
1lk9.a
1lk9.b
2hor.a
2hox.a
[1] 1lk9.a
0
0.3 0.3 0.2
[1] 1lk9.b 0.3
0
0.4 0.3
[1] 2hor.a 0.3 0.4
0
0.2
[1] 2hox.a 0.2 0.3 0.2
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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