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ARLY2_ANAPL_4_468

Argininosuccinate lyase [Lyase 1 family. Argininosuccinate lyase subfamily]

Composition of the binding site

Protein chains homotrimer [domain annotation]
A1 (ARLY2_ANAPL):R: Substrate binding (114:116)
29, 91, 119, 205, 206, 323, 325, 328, 331
29, 91, 114:116, 119, 205, 206, 323, 325, 328, 331
A2 (ARLY2_ANAPL):281, 289, 291281, 289, 291
A3 (ARLY2_ANAPL):161, 162, 166, 167161, 162, 166, 167

Full PDB list

1auw, 1dcn, 1hy1, 1k7w, 1tju, 1tjv, 1tjw

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1 A2 A3
S
2
9
H
9
1
S
1
1
4
R
1
1
5
N
1
1
6
V
1
1
9
A
2
0
5
L
2
0
6
Y
3
2
3
Q
3
2
8
K
3
3
1
T
2
8
1
N
2
9
1
T
1
6
1
H
1
6
2
A
1
6
6
[1]1auw.a none . N . . . . . . . . . . . . . .
[1]1dcn.a none - . . . . . . . . . . . . . N .
[1]1dcn.d as120 . . . . . . . . . . . . . . N .
[1]1hy1.c none . . . . . . . . . . . . . . . .
[1]1k7w.b as120 . . . . . . . . . . . . . . . .
[1]1tju.a none . . . . . . . . . . . . . S . .
[1]1tjv.a none . . . . . . . . . . . . . D . .
[1]1tjw.b as120 . . . . . . . . . . . . . D . .

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 A2 A3
S
2
9
H
9
1
S
1
1
4
R
1
1
5
N
1
1
6
V
1
1
9
A
2
0
5
L
2
0
6
Y
3
2
3
K
3
2
5
Q
3
2
8
K
3
3
1
T
2
8
1
K
2
8
9
N
2
9
1
T
1
6
1
H
1
6
2
A
1
6
6
Q
1
6
7
[1]1auw.a . N . . . . . . . . . . . . . . . . .
[1]1dcn.a - . . * . . . . . . . . . - . . N . .
[1]1dcn.d . . . . . . . . . . . . . - . . N . .
[1]1hy1.c . . . . . . . . . . . . . . . . . . .
[1]1k7w.b . . . . . . . . . . . . . . . . . . .
[1]1tju.a . . . . . . . . . . . . . . . S . . .
[1]1tjv.a . . . . . . . . . . . . . . . D . . .
[1]1tjw.b . . . . . . . . . . . . . . . D . . .

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
1auw.a is apo
1dcn.a is apo
1dcn.d:as1
1hy1.c is apo
1k7w.b:as1
1tju.a is apo
1tjv.a is apo
1tjw.b:as1
[1] 1auw.a
-
- 0.2 - 0.2 - - 0.2
[1] 1dcn.a -
-
2.6 - 0.7 - - 3.6
[1] 1dcn.d - -
0
- 0.2 - - 0.1
[1] 1hy1.c - - 0.1
-
0.2 - - 0.3
[1] 1k7w.b - - 0 -
0
- - 0.3
[1] 1tju.a - - 0 - 0
-
- 0
[1] 1tjv.a - - 0.3 - 0.2 -
-
0
[1] 1tjw.b - - 0.1 - 0.1 - -
0.3
[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
1auw.a
1dcn.a
1dcn.d
1hy1.c
1k7w.b
1tju.a
1tjv.a
1tjw.b
[1] 1auw.a
0
.21 .03 .02 .02 .02 .03 .03
[1] 1dcn.a .21
0
.19 .20 .18 .19 .21 .20
[1] 1dcn.d .03 .19
0
.04 .02 .02 .02 .02
[1] 1hy1.c .02 .20 .04
0
.03 .02 .04 .03
[1] 1k7w.b .02 .18 .02 .03
0
.02 .03 .02
[1] 1tju.a .02 .19 .02 .02 .02
0
.02 .02
[1] 1tjv.a .03 .21 .02 .04 .03 .02
0
.03
[1] 1tjw.b .03 .20 .02 .03 .02 .02 .03
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 1.1 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
1auw.a
1dcn.a
1dcn.d
1hy1.c
1k7w.b
1tju.a
1tjv.a
1tjw.b
[1] 1auw.a
0
0.7 0.8 0.5 0.5 0.5 0.4 0.5
[1] 1dcn.a 0.7
0
0.7 0.6 0.7 0.6 0.7 0.7
[1] 1dcn.d 0.8 0.7
0
0.8 0.6 0.8 0.8 0.7
[1] 1hy1.c 0.5 0.6 0.8
0
0.6 0.5 0.5 0.6
[1] 1k7w.b 0.5 0.7 0.6 0.6
0
0.5 0.5 0.2
[1] 1tju.a 0.5 0.6 0.8 0.5 0.5
0
0.3 0.5
[1] 1tjv.a 0.4 0.7 0.8 0.5 0.5 0.3
0
0.4
[1] 1tjw.b 0.5 0.7 0.7 0.6 0.2 0.5 0.4
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

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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
1auw.a
1dcn.a
1dcn.d
1hy1.c
1k7w.b
1tju.a
1tjv.a
1tjw.b
[1] 1auw.a
0
1.9 1.1 0.9 1.2 1.0 0.8 0.9
[1] 1dcn.a 1.9
0
1.7 1.9 1.5 1.9 1.9 1.9
[1] 1dcn.d 1.1 1.7
0
1.2 1.3 1.1 1.2 1.0
[1] 1hy1.c 0.9 1.9 1.2
0
1.2 0.9 0.8 1.0
[1] 1k7w.b 1.2 1.5 1.3 1.2
0
1.1 1.2 1.0
[1] 1tju.a 1.0 1.9 1.1 0.9 1.1
0
0.7 0.8
[1] 1tjv.a 0.8 1.9 1.2 0.8 1.2 0.7
0
0.9
[1] 1tjw.b 0.9 1.9 1.0 1.0 1.0 0.8 0.9
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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