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AGM1_CANAX_1_544

Phosphoacetylglucosamine mutase [Phosphohexose mutase family]

Composition of the binding site

Protein chains monomer [domain annotation]
A1 (AGM1_CANAX):R: Substrate binding (387, 389)
R: Substrate binding (512, 514:516)
26, 295, 346, 368:370, 391, 521
26, 295, 346, 368:370, 387, 389, 391, 512, 514:516, 521
Metals (Me):Zn

Full PDB list

2dka, 2dkc, 2dkd

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1 Me
T
2
6
R
2
9
5
Y
3
4
6
T
3
6
8
G
3
6
9
V
3
7
0
E
3
8
7
N
3
8
9
H
3
9
1
R
5
1
2
S
5
1
4
G
5
1
5
T
5
1
6
R
5
2
1
[1]2dka.a none . . . . . . . . . . . - - .
[1]2dkc.b 16g19 . . . . . . . . . . . . . . Zn
[1]2dkd.a ng119 . . . . . . . . . . . . . . Zn

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 Me
T
2
6
R
2
9
5
Y
3
4
6
T
3
6
8
G
3
6
9
V
3
7
0
E
3
8
7
N
3
8
9
H
3
9
1
R
5
1
2
S
5
1
4
G
5
1
5
T
5
1
6
R
5
2
1
[1]2dka.a . . . . . . . . . . . - - .
[1]2dkc.b . . . . . . . . . . . . . . Zn
[1]2dkd.a . . . . . . . . . . . . . . Zn

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
2dka.a is apo
2dkc.b:16g
2dkd.a:ng1
[1] 2dka.a
-
0.1 0
[1] 2dkc.b -
0.1
0.5
[1] 2dkd.a - 0.1
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
2dka.a
2dkc.b
2dkd.a
[1] 2dka.a
0
.04 0
[1] 2dkc.b .04
0
.04
[1] 2dkd.a 0 .04
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 1.0 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
2dka.a
2dkc.b
2dkd.a
[1] 2dka.a
0
0.9 0.9
[1] 2dkc.b 0.9
0
0.5
[1] 2dkd.a 0.9 0.5
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

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
2dka.a
2dkc.b
2dkd.a
[1] 2dka.a
0
1.2 1.2
[1] 2dkc.b 1.2
0
1.0
[1] 2dkd.a 1.2 1.0
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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