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ASSY_THET8_1_400

Argininosuccinate synthase [Argininosuccinate synthase family. Type 1 subfamily]

Composition of the binding site

Protein chains monomer
A1 (ASSY_THET8):6:14, 31:33, 35, 37, 84, 88, 89, 92, 95, 113:116, 119:121, 124, 125, 173:175, 182:184, 258, 260, 270, 3106:14, 31:33, 35, 37, 84, 88, 89, 92, 95, 113:116, 119:121, 124, 125, 173:175, 182:184, 258, 260, 270, 310

Full PDB list

1j1z, 1j20, 1j21, 1kh1, 1kh2, 1kh3, 1kor

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1
A
6
Y
7
S
8
G
1
0
L
1
1
D
1
2
T
1
3
F
3
1
T
3
2
A
3
3
Q
3
7
Y
8
4
T
8
8
S
8
9
R
9
2
I
9
5
H
1
1
3
G
1
1
4
A
1
1
5
T
1
1
6
G
1
1
9
N
1
2
0
D
1
2
1
R
1
2
4
F
1
2
5
S
1
7
3
M
1
7
4
D
1
7
5
S
1
8
2
Y
1
8
3
E
1
8
4
E
2
5
8
Y
2
7
0
Y
3
1
0
[1]1j1z.a atp-cir-D-D-D-D79 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]1j1z.b atp,atp-cir-D-D-D-D,cir122 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]1j20.d amp,as143 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]1j21.a atp-cir43 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]1j21.b atp,cir43 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]1kh1.a none . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]1kh2.a atp31 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]1kh3.a anp-R-RR-RD-DD-D115 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]1kh3.b anp,anp-R-RR-RD-DD-D146 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]1kor.a anp-R43 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]1kor.b anp,R43 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

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
A
6
Y
7
S
8
G
9
G
1
0
L
1
1
D
1
2
T
1
3
S
1
4
F
3
1
T
3
2
A
3
3
I
3
5
Q
3
7
Y
8
4
T
8
8
S
8
9
R
9
2
I
9
5
H
1
1
3
G
1
1
4
A
1
1
5
T
1
1
6
G
1
1
9
N
1
2
0
D
1
2
1
R
1
2
4
F
1
2
5
S
1
7
3
M
1
7
4
D
1
7
5
S
1
8
2
Y
1
8
3
E
1
8
4
E
2
5
8
R
2
6
0
Y
2
7
0
Y
3
1
0
[1]1j1z.a . . . . . . . * . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]1j1z.b . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]1j20.d . . . . . . . * . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]1j21.a . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]1j21.b . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]1kh1.a . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]1kh2.a . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]1kh3.a . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]1kh3.b . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]1kor.a . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]1kor.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
1j1z.a:atp-cir-D-D-D-D
1j1z.b:atp,atp-cir-D-D-D-D,cir
1j20.d:amp,as1
1j21.a:atp-cir
1j21.b:atp,cir
1kh1.a is apo
1kh2.a:atp
1kh3.a:anp-R-RR-RD-DD-D
1kh3.b:anp,anp-R-RR-RD-DD-D
1kor.a:anp-R
1kor.b:R,anp
[1] 1j1z.a
0.1
1.0 0.7 1.1 1.8 - 1.7 1.1 1.1 0.9 1.5
[1] 1j1z.b 0
0.2
0.7 0.6 1.2 - 0.8 0.9 0.9 0.4 0.8
[1] 1j20.d 0.5 1.9
0.2
1.6 2.5 - 2.3 1.5 1.3 1.6 2.9
[1] 1j21.a 0.2 0.2 0.4
0.2
0.6 - 0.6 0.7 0.4 0.3 0.6
[1] 1j21.b 0.1 0.3 0.4 0.2
0.2
- 0.4 0.9 0.3 0.1 0.1
[1] 1kh1.a 0.8 1.0 0.5 1.1 1.7
-
1.1 1.2 1.1 1.3 1.3
[1] 1kh2.a 0.6 0.5 0.7 0.4 0.9 -
0.5
1.0 0.6 0.2 0.7
[1] 1kh3.a 0.1 0.2 0.7 0.2 0.7 - 0.5
0.6
0.4 0.1 0.5
[1] 1kh3.b 0.1 0.2 0.6 0.1 0.3 - 0.4 0.5
0.3
0 0.1
[1] 1kor.a 0 0.2 0.7 0.3 0.7 - 1.0 1.2 0.9
0.4
0.7
[1] 1kor.b 0 0.2 0.7 0.2 0.5 - 0.5 1.0 0.5 0.1
0.2
[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
1j1z.a
1j1z.b
1j20.d
1j21.a
1j21.b
1kh1.a
1kh2.a
1kh3.a
1kh3.b
1kor.a
1kor.b
[1] 1j1z.a
0
.03 .06 .06 .07 .06 .05 .05 .06 .04 .07
[1] 1j1z.b .03
0
.09 .04 .05 .05 .03 .03 .03 .02 .04
[1] 1j20.d .06 .09
0
.09 .09 .09 .08 .09 .10 .08 .11
[1] 1j21.a .06 .04 .09
0
.04 .04 .03 .03 .03 .04 .04
[1] 1j21.b .07 .05 .09 .04
0
.07 .05 .04 .03 .04 .03
[1] 1kh1.a .06 .05 .09 .04 .07
0
.03 .06 .06 .06 .08
[1] 1kh2.a .05 .03 .08 .03 .05 .03
0
.04 .04 .03 .05
[1] 1kh3.a .05 .03 .09 .03 .04 .06 .04
0
.02 .03 .04
[1] 1kh3.b .06 .03 .10 .03 .03 .06 .04 .02
0
.04 .03
[1] 1kor.a .04 .02 .08 .04 .04 .06 .03 .03 .04
0
.03
[1] 1kor.b .07 .04 .11 .04 .03 .08 .05 .04 .03 .03
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
1j1z.a
1j1z.b
1j20.d
1j21.a
1j21.b
1kh1.a
1kh2.a
1kh3.a
1kh3.b
1kor.a
1kor.b
[1] 1j1z.a
0
0.3 0.4 0.5 0.7 0.5 0.5 0.4 0.6 0.2 0.5
[1] 1j1z.b 0.3
0
0.5 0.3 0.5 0.5 0.4 0.2 0.3 0.2 0.2
[1] 1j20.d 0.4 0.5
0
0.5 0.8 0.5 0.6 0.5 0.7 0.4 0.6
[1] 1j21.a 0.5 0.3 0.5
0
0.3 0.5 0.3 0.2 0.3 0.3 0.2
[1] 1j21.b 0.7 0.5 0.8 0.3
0
0.7 0.5 0.4 0.3 0.5 0.3
[1] 1kh1.a 0.5 0.5 0.5 0.5 0.7
0
0.3 0.5 0.6 0.4 0.5
[1] 1kh2.a 0.5 0.4 0.6 0.3 0.5 0.3
0
0.4 0.4 0.4 0.4
[1] 1kh3.a 0.4 0.2 0.5 0.2 0.4 0.5 0.4
0
0.2 0.2 0.2
[1] 1kh3.b 0.6 0.3 0.7 0.3 0.3 0.6 0.4 0.2
0
0.4 0.2
[1] 1kor.a 0.2 0.2 0.4 0.3 0.5 0.4 0.4 0.2 0.4
0
0.3
[1] 1kor.b 0.5 0.2 0.6 0.2 0.3 0.5 0.4 0.2 0.2 0.3
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 0.4 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
1j1z.a
1j1z.b
1j20.d
1j21.a
1j21.b
1kh1.a
1kh2.a
1kh3.a
1kh3.b
1kor.a
1kor.b
[1] 1j1z.a
0
0.4 0.4 0.5 0.7 0.5 0.6 0.4 0.6 0.3 0.5
[1] 1j1z.b 0.4
0
0.5 0.4 0.5 0.6 0.5 0.3 0.3 0.3 0.2
[1] 1j20.d 0.4 0.5
0
0.6 0.8 0.6 0.7 0.6 0.7 0.5 0.6
[1] 1j21.a 0.5 0.4 0.6
0
0.4 0.5 0.4 0.2 0.4 0.3 0.3
[1] 1j21.b 0.7 0.5 0.8 0.4
0
0.7 0.6 0.5 0.3 0.6 0.3
[1] 1kh1.a 0.5 0.6 0.6 0.5 0.7
0
0.4 0.5 0.7 0.5 0.6
[1] 1kh2.a 0.6 0.5 0.7 0.4 0.6 0.4
0
0.5 0.5 0.5 0.5
[1] 1kh3.a 0.4 0.3 0.6 0.2 0.5 0.5 0.5
0
0.3 0.2 0.3
[1] 1kh3.b 0.6 0.3 0.7 0.4 0.3 0.7 0.5 0.3
0
0.4 0.2
[1] 1kor.a 0.3 0.3 0.5 0.3 0.6 0.5 0.5 0.2 0.4
0
0.3
[1] 1kor.b 0.5 0.2 0.6 0.3 0.3 0.6 0.5 0.3 0.2 0.3
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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