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ARGB_ECOLI_1_258

Acetylglutamate kinase [Acetylglutamate kinase family. ArgB subfamily]

Composition of the binding site

Protein chains monomer [domain annotation]
A1 (ARGB_ECOLI):R: Substrate binding (44, 45)
8:11, 43, 65, 66, 80, 122, 147, 158:162, 180:182, 184:186, 209:217
8:11, 43:45, 65, 66, 80, 122, 147, 158:162, 180:182, 184:186, 209:217

Full PDB list

1gs5, 1gsj, 1oh9, 1oha, 1ohb, 2wxb, 2x2w

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1
K
8
G
1
0
G
1
1
G
4
3
G
4
4
G
4
5
L
6
5
R
6
6
L
8
0
V
1
2
2
S
1
4
7
N
1
5
8
V
1
5
9
N
1
6
0
A
1
6
1
S
1
8
0
D
1
8
1
V
1
8
2
G
1
8
4
I
1
8
5
L
1
8
6
I
2
0
9
I
2
1
0
T
2
1
1
D
2
1
2
G
2
1
3
M
2
1
4
K
2
1
7
[1]1gs5.a anp,nlg44 . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]1gsj.a anp,nlg44 . . . . . . . . . . . . . . . . . . . . . . . . . . * .
[1]1oh9.a adp,alf,mg,nlg46 . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]1oha.a adp,nlg40 . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]1ohb.a adp27 . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]2wxb.b dtu8 . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]2x2w.b x2w17 . . . . . . . . . . . . . . . . . . . . . . . . . . . .

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
K
8
L
9
G
1
0
G
1
1
G
4
3
G
4
4
G
4
5
L
6
5
R
6
6
L
8
0
V
1
2
2
S
1
4
7
N
1
5
8
V
1
5
9
N
1
6
0
A
1
6
1
D
1
6
2
S
1
8
0
D
1
8
1
V
1
8
2
G
1
8
4
I
1
8
5
L
1
8
6
I
2
0
9
I
2
1
0
T
2
1
1
D
2
1
2
G
2
1
3
M
2
1
4
I
2
1
5
V
2
1
6
K
2
1
7
[1]1gs5.a . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]1gsj.a . . . . . . . . . . . . . . . . . . . . . . . . . . . . * . . .
[1]1oh9.a . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]1oha.a . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]1ohb.a . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]2wxb.b . . . . . . . . . . . . . . . . . . . . . . . . . . . * * * . .
[1]2x2w.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
1gs5.a:anp,nlg
1gsj.a:anp,nlg
1oh9.a:adp,alf,mg,nlg
1oha.a:adp,nlg
1ohb.a:adp
2wxb.b:dtu
2x2w.b:x2w
[1] 1gs5.a
0.1
0.2 0.1 0.1 0.2 0 0
[1] 1gsj.a 0.2
0.2
0.3 0.5 0.2 0 0.1
[1] 1oh9.a 0.3 0.2
0.1
0.1 0.6 0.3 0.1
[1] 1oha.a 0.6 0.8 0.4
0
2.0 0.3 0.1
[1] 1ohb.a 0.3 0.2 0.4 0.4
0
0 0.1
[1] 2wxb.b 5.2 5.6 5.1 5.1 5.4
0
0
[1] 2x2w.b 5.2 5.6 5.8 4.7 5.5 0
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
1gs5.a
1gsj.a
1oh9.a
1oha.a
1ohb.a
2wxb.b
2x2w.b
[1] 1gs5.a
0
.02 .02 .07 .03 .19 .22
[1] 1gsj.a .02
0
.03 .08 .03 .21 .24
[1] 1oh9.a .02 .03
0
.06 .04 .20 .23
[1] 1oha.a .07 .08 .06
0
.09 .23 .25
[1] 1ohb.a .03 .03 .04 .09
0
.21 .23
[1] 2wxb.b .19 .21 .20 .23 .21
0
.05
[1] 2x2w.b .22 .24 .23 .25 .23 .05
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 0.9 Å)

Pockets (x) vs pockets (y) colored by RMSD of site residue backbone atoms

zoom: [−] [+]; [view as image]; [download as text]

pocketpocket
≥10 Å
9 Å
8 Å
7 Å
6 Å
5 Å
4 Å
3 Å
2 Å
1 Å
0 Å
1gs5.a
1gsj.a
1oh9.a
1oha.a
1ohb.a
2wxb.b
2x2w.b
[1] 1gs5.a
0
0.2 0.2 0.6 0.7 4.2 4.4
[1] 1gsj.a 0.2
0
0.2 0.7 0.6 4.3 4.5
[1] 1oh9.a 0.2 0.2
0
0.6 0.8 4.2 4.4
[1] 1oha.a 0.6 0.7 0.6
0
1.2 4.1 4.3
[1] 1ohb.a 0.7 0.6 0.8 1.2
0
4.5 4.7
[1] 2wxb.b 4.2 4.3 4.2 4.1 4.5
0
0.8
[1] 2x2w.b 4.4 4.5 4.4 4.3 4.7 0.8
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 0.8 Å)

Pockets (x) vs pockets (y) colored by RMSD of all site residue atoms

zoom: [−] [+]; [view as image]; [download as text]

pocketpocket
≥10 Å
9 Å
8 Å
7 Å
6 Å
5 Å
4 Å
3 Å
2 Å
1 Å
0 Å
1gs5.a
1gsj.a
1oh9.a
1oha.a
1ohb.a
2wxb.b
2x2w.b
[1] 1gs5.a
0
0.5 0.4 0.8 0.8 4.4 4.7
[1] 1gsj.a 0.5
0
0.6 0.9 0.8 4.5 4.8
[1] 1oh9.a 0.4 0.6
0
0.7 0.9 4.4 4.7
[1] 1oha.a 0.8 0.9 0.7
0
1.3 4.4 4.6
[1] 1ohb.a 0.8 0.8 0.9 1.3
0
4.8 5.1
[1] 2wxb.b 4.4 4.5 4.4 4.4 4.8
0
1.2
[1] 2x2w.b 4.7 4.8 4.7 4.6 5.1 1.2
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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