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F16P1_PIG_2_337_allosteric

Fructose-1,6-bisphosphatase 1 [FBPase class 1 family]

Composition of the binding site

Protein chains monomer
A1 (F16P1_PIG):17:19, 21, 22, 25:32, 35, 113, 114, 141, 161, 162, 176, 178, 17917:19, 21, 22, 25:32, 35, 113, 114, 141, 161, 162, 176, 178, 179

Full PDB list

1cnq, 1eyi, 1eyj, 1eyk, 1fbc, 1fbd, 1fbe, 1fbf, 1fbg, 1fbh, 1fbp, 1fj6, 1fj9, 1fpb, 1fpd, 1fpe, 1fpf, 1fpg, 1fpi, 1fpj, 1fpk, 1fpl, 1frp, 1fsa, 1kz8, 1lev, 1nuw, 1nux, 1nuy, 1nuz, 1nv0, 1nv1, 1nv2, 1nv3, 1nv4, 1nv5, 1nv6, 1nv7, 1q9d, 1rdx, 1rdy, 1rdz, 1yxi, 1yyz, 1yz0, 2f3b, 2f3d, 2fbp, 2qvu, 2qvv, 3fbp, 4fbp, 4gbv, 4gbw, 4gws, 4gwu, 4gww, 4gwx, 4gwy, 4gwz, 4gx3, 4gx4, 4gx6, 4h45, 4h46, 4kxp, 5fbp (redundant Pocketome entry)

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1
F
1
7
V
1
8
E
2
1
G
2
2
A
2
5
G
2
7
T
2
8
G
2
9
E
3
0
M
3
1
T
3
2
L
3
5
K
1
1
3
Y
1
1
4
R
1
4
1
V
1
6
1
A
1
6
2
L
1
7
6
M
1
7
8
V
1
7
9
[1]1cnq.a f6p16 . . . . . . . . . . . . . . . . . . . .
[1]1fbc.b none . . Q . . . . . . . . . . . . . . . . .
[1]1fpb.a fdp20 . . Q . . . . . . . . . . . . . . . . .
[1]1lev.a cli19 . . . . . . . . . . . . . . . . . . . .
[1]1rdz.a amp23 . . Q . . . . . . . . . . . . . . . . .
[1]2f3b.a none . . . . . . . . . . . . . . . . . . . .
[1]2f3d.a amp23 . . . . . . . . . . . . . . . . . . . .
[1]4gww.a f6p16 . . . . . . . . . . . . . . . . . . . .
[1]4gwx.a none . . . . . . . . . . . . . . . . . . . .
[1]4gwy.a amp23 . . . . . . . . . . . . . . . . . . . .
[1]4gwz.b amp23 . . . . . . . . . . . . . . . . . . . .
[1]5fbp.a f6p16 . . Q . . . . . . . . . . . . . . . . .

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
F
1
7
V
1
8
M
1
9
E
2
1
G
2
2
A
2
5
R
2
6
G
2
7
T
2
8
G
2
9
E
3
0
M
3
1
T
3
2
L
3
5
K
1
1
3
Y
1
1
4
R
1
4
1
V
1
6
1
A
1
6
2
L
1
7
6
M
1
7
8
V
1
7
9
[1]1cnq.a . . . . . . . . . . . . . . * . . . . . . .
[1]1fbc.b . . . Q . . . . * . . . . . * . . . . . . .
[1]1fpb.a . . . Q . . . . . . . . . . * . . . . . . .
[1]1lev.a . . . . . . . . . . . . . . . . . . . . . .
[1]1rdz.a . . . Q . . . . . . . . . . . . . . . . . .
[1]2f3b.a . . . . . . . . . . . . . . * . . . . . * .
[1]2f3d.a . . . . . . . . . . . . . . . . . . . . * .
[1]4gww.a . . K . . . . . * * . . . . * . . . . . . .
[1]4gwx.a . . W . . . . . . . . . . . * . . . . . . .
[1]4gwy.a . . K . . . . . . . . . . . . . . . . . * .
[1]4gwz.b . . W . . . . . . . . * . . . . . . . . . .
[1]5fbp.a . . . Q . . . . . . . . . . * . . . . . . .

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
1cnq.a:f6p
1fbc.b is apo
1fpb.a:fdp
1lev.a:cli
1rdz.a:amp
2f3b.a is apo
2f3d.a:amp
4gww.a:f6p
4gwx.a is apo
4gwy.a:amp
4gwz.b:amp
5fbp.a:f6p
[1] 1cnq.a
0
- 0.2 1.1 2.1 - 2.0 0.2 - 1.8 1.6 0.3
[1] 1fbc.b 0.6
-
0.7 1.5 2.2 - 2.4 0.2 - 1.4 1.6 0.7
[1] 1fpb.a 0 -
0.1
0.8 1.8 - 2.1 0.1 - 1.6 1.7 0.1
[1] 1lev.a 0.2 - 0.6
0
1.6 - 1.9 0.2 - 1.0 0.5 0.3
[1] 1rdz.a 0.8 - 0.6 0.8
0.1
- 0.1 0.4 - 0.1 0.2 0.4
[1] 2f3b.a 0 - 0.2 1.4 1.8
-
2.1 0.3 - 2.1 1.5 0.5
[1] 2f3d.a 0.8 - 0.7 0.9 0.2 -
0.1
0.8 - 0.5 0.4 0.5
[1] 4gww.a 0.7 - 1.0 1.8 2.3 - 2.6
0.2
- 1.6 1.9 1.1
[1] 4gwx.a 0.1 - 0.4 1.0 2.0 - 1.7 0.4
-
1.4 1.7 0.3
[1] 4gwy.a 1.0 - 0.9 1.1 0.5 - 0.7 0.7 -
0.5
0.8 0.8
[1] 4gwz.b 1.0 - 1.0 0.8 0.6 - 0.7 0.8 - 0.5
0.1
1.0
[1] 5fbp.a 0 - 0.3 0.8 1.6 - 1.9 0.1 - 1.8 1.4
0.1
[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
1cnq.a
1fbc.b
1fpb.a
1lev.a
1rdz.a
2f3b.a
2f3d.a
4gww.a
4gwx.a
4gwy.a
4gwz.b
5fbp.a
[1] 1cnq.a
0
.11 .09 .14 .17 .07 .16 .09 .06 .17 .17 .07
[1] 1fbc.b .11
0
.12 .15 .17 .13 .18 .13 .11 .19 .18 .11
[1] 1fpb.a .09 .12
0
.18 .17 .06 .13 .12 .05 .15 .16 .02
[1] 1lev.a .14 .15 .18
0
.18 .17 .17 .16 .15 .18 .15 .16
[1] 1rdz.a .17 .17 .17 .18
0
.17 .04 .21 .18 .07 .07 .16
[1] 2f3b.a .07 .13 .06 .17 .17
0
.17 .14 .08 .15 .14 .05
[1] 2f3d.a .16 .18 .13 .17 .04 .17
0
.20 .14 .05 .10 .14
[1] 4gww.a .09 .13 .12 .16 .21 .14 .20
0
.09 .20 .22 .13
[1] 4gwx.a .06 .11 .05 .15 .18 .08 .14 .09
0
.15 .17 .05
[1] 4gwy.a .17 .19 .15 .18 .07 .15 .05 .20 .15
0
.09 .16
[1] 4gwz.b .17 .18 .16 .15 .07 .14 .10 .22 .17 .09
0
.15
[1] 5fbp.a .07 .11 .02 .16 .16 .05 .14 .13 .05 .16 .15
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 1.4 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
1cnq.a
1fbc.b
1fpb.a
1lev.a
1rdz.a
2f3b.a
2f3d.a
4gww.a
4gwx.a
4gwy.a
4gwz.b
5fbp.a
[1] 1cnq.a
0
0.9 1.1 1.1 1.1 1.0 1.2 1.1 0.7 1.1 1.1 1.0
[1] 1fbc.b 0.9
0
0.7 0.7 0.9 0.6 1.1 0.9 0.7 0.9 0.8 0.8
[1] 1fpb.a 1.1 0.7
0
0.8 0.9 0.7 1.0 1.1 0.7 1.2 1.0 0.3
[1] 1lev.a 1.1 0.7 0.8
0
0.6 0.6 0.8 0.8 0.8 0.7 0.5 0.8
[1] 1rdz.a 1.1 0.9 0.9 0.6
0
1.0 0.4 1.1 0.9 0.6 0.5 1.0
[1] 2f3b.a 1.0 0.6 0.7 0.6 1.0
0
1.2 0.7 0.7 1.0 0.8 0.8
[1] 2f3d.a 1.2 1.1 1.0 0.8 0.4 1.2
0
1.4 1.0 0.8 0.8 1.1
[1] 4gww.a 1.1 0.9 1.1 0.8 1.1 0.7 1.4
0
1.0 0.9 0.9 1.2
[1] 4gwx.a 0.7 0.7 0.7 0.8 0.9 0.7 1.0 1.0
0
1.0 0.9 0.7
[1] 4gwy.a 1.1 0.9 1.2 0.7 0.6 1.0 0.8 0.9 1.0
0
0.5 1.2
[1] 4gwz.b 1.1 0.8 1.0 0.5 0.5 0.8 0.8 0.9 0.9 0.5
0
1.1
[1] 5fbp.a 1.0 0.8 0.3 0.8 1.0 0.8 1.1 1.2 0.7 1.2 1.1
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 0.9 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
1cnq.a
1fbc.b
1fpb.a
1lev.a
1rdz.a
2f3b.a
2f3d.a
4gww.a
4gwx.a
4gwy.a
4gwz.b
5fbp.a
[1] 1cnq.a
0
1.9 1.4 1.8 1.8 1.5 1.5 1.6 1.2 1.6 1.9 1.5
[1] 1fbc.b 1.9
0
1.5 1.4 1.5 1.2 1.7 1.8 1.5 1.8 1.4 1.4
[1] 1fpb.a 1.4 1.5
0
1.3 1.4 0.9 1.6 1.2 0.8 1.3 1.6 0.6
[1] 1lev.a 1.8 1.4 1.3
0
1.2 1.2 1.6 1.4 1.4 1.4 0.9 1.4
[1] 1rdz.a 1.8 1.5 1.4 1.2
0
1.3 1.5 1.5 1.3 1.2 0.9 1.5
[1] 2f3b.a 1.5 1.2 0.9 1.2 1.3
0
1.6 1.1 0.9 1.3 1.3 1.0
[1] 2f3d.a 1.5 1.7 1.6 1.6 1.5 1.6
0
2.0 1.6 1.6 1.6 1.6
[1] 4gww.a 1.6 1.8 1.2 1.4 1.5 1.1 2.0
0
1.1 1.1 1.5 1.4
[1] 4gwx.a 1.2 1.5 0.8 1.4 1.3 0.9 1.6 1.1
0
1.2 1.7 0.9
[1] 4gwy.a 1.6 1.8 1.3 1.4 1.2 1.3 1.6 1.1 1.2
0
1.3 1.4
[1] 4gwz.b 1.9 1.4 1.6 0.9 0.9 1.3 1.6 1.5 1.7 1.3
0
1.6
[1] 5fbp.a 1.5 1.4 0.6 1.4 1.5 1.0 1.6 1.4 0.9 1.4 1.6
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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