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F16P1_PIG_2_337_catalytic

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

Composition of the binding site

Protein chains homodimer [domain annotation]
A1 (F16P1_PIG):R: Substrate binding (122:125)
R: Substrate binding (213, 216)
R: Substrate binding (245, 247:249)
R: Substrate binding (275:277)
69, 98, 119, 121, 126, 252, 263, 265, 270, 281
69, 98, 119, 121:126, 213, 216, 245, 247:249, 252, 263, 265, 270, 275:277, 281
A2 (F16P1_PIG):R: Substrate binding (244)
243
243, 244
Metals (Me):Mg/Mn/Tl/Zn/K

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 A2 Me
D
6
9
E
9
8
D
1
2
2
G
1
2
3
S
1
2
4
S
1
2
5
N
2
1
3
Y
2
1
6
Y
2
4
5
G
2
4
7
S
2
4
8
M
2
4
9
Y
2
6
5
K
2
7
5
L
2
7
6
R
2
7
7
E
2
8
1
R
2
4
4
[1]1fbg.a ahm19 - . . . . . . . . . . . . . . . . . Mn
[1]1fbh.a afp,fbp40 . . . . . . . . . . . . . . . . . .
[1]1fj6.a f6p,zn17 . . . . . . . . . . . . . . . . . . Zn
[1]1fpd.a ahg19 - . . . . . . . . . . . . . . . . . Mn
[1]1fpi.a ahg,k20 - . . . . . . . . . . . . . . . . . K
[1]1fpj.a ahg,tl20 - . . . . . . . . . . . . . . . . . Tl
[1]1fpk.a tl1 - . . . . . . . . . . . . . . . . . Tl
[1]1nuw.a f6p,mg17 . . . . . . . . . . . . . . . . . . Mg
[1]1nv2.a f6p,tl17 . . . . . . . . . . . . . . . . . . Mg
[1]1rdz.a f6p16 . . . . . . . . . . . . . . . . . A
[1]2qvu.a fdp,mg21 . . . . . . . . . . . . . . . . . . Mg
[1]2qvv.a fdp20 . . . . . . . . . . . . . . . . . . Zn
[1]4fbp.a none - . . . . . . . . . . . . . . . . .
[1]4gbw.a f6p,mn17 . . . . . . . . . . . . . . . . . . Mn
[1]4gww.a f6p16 - . . . . . . . . . . . . . . . . . Mg

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 Me
D
6
9
E
9
8
D
1
1
9
L
1
2
1
D
1
2
2
G
1
2
3
S
1
2
4
S
1
2
5
N
1
2
6
N
2
1
3
Y
2
1
6
Y
2
4
5
G
2
4
7
S
2
4
8
M
2
4
9
D
2
5
2
F
2
6
3
Y
2
6
5
K
2
7
0
K
2
7
5
L
2
7
6
R
2
7
7
E
2
8
1
A
2
4
3
R
2
4
4
[1]1fbg.a - . . . . . . . . . . . . . . . . . . . . * . . . Mn
[1]1fbh.a . . . . . . . . . . . . . . . . . . . . . * . . .
[1]1fj6.a . . . . . . . . . . . . . . . . . . . . . * . . . Zn
[1]1fpd.a - . . . . . . . . . . . . . . . . . . . . * . . . Mn
[1]1fpi.a - . . . . . . . . . . . . . . . . . . . . . . . . K
[1]1fpj.a - . . . . . . . . . . . . . . . . . . . . . . . . Tl
[1]1fpk.a - . . . . . . . . . . . . . . . . . . . . * . . . Tl
[1]1nuw.a * . . . . . * . . . . . . . . . . . . . . * . . . Mg
[1]1nv2.a . . . . . . . . . . . . . . . . . . . . . . . . . Mg
[1]1rdz.a . . . . . . . . . . . . . . . . . . . . . * . . A
[1]2qvu.a . . . . . . . . . . . . . . . . . . . . . * . . . Mg
[1]2qvv.a . . . . . . . . . . . . . . . . . . . . . * . . . Zn
[1]4fbp.a - . . . . . . . . . . . . . . . . . . * . * . . .
[1]4gbw.a . . . . . . . . . . . . . . . . . . . . . * . . . Mn
[1]4gww.a - . . . . . . . . . . . . . . . . . . . . . . . . Mg

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
1fbg.a:ahm
1fbh.a:afp,fbp
1fj6.a:f6p,zn
1fpd.a:ahg
1fpi.a:ahg,k
1fpj.a:ahg,tl
1fpk.a:tl
1nuw.a:f6p,mg
1nv2.a:f6p,tl
1rdz.a:f6p
2qvu.a:fdp,mg
2qvv.a:fdp
4fbp.a is apo
4gbw.a:f6p,mn
4gww.a:f6p
[1] 1fbg.a
0.3
0.5 0 0.2 1.2 0.7 0.2 0.2 0.8 0.1 0.4 0.5 - 0.3 0.2
[1] 1fbh.a 0.8
0.4
0 0.1 1.6 0.9 0.1 0 0.9 0.1 0.1 0.2 - 0 0.1
[1] 1fj6.a 0.3 0.9
0.3
0.3 2.1 1.2 0 0.1 1.0 0.2 0.4 0.2 - 0.3 0.4
[1] 1fpd.a 0.9 0.4 0.1
0.1
1.6 1.0 0.1 0.1 1.1 0.2 0.1 0.2 - 0.1 0.3
[1] 1fpi.a 1.0 0.3 0.1 0.1
0
0 0 0.1 0.1 0.2 0.3 0.3 - 0.3 0.3
[1] 1fpj.a 0.9 0.3 0.1 0.1 0.1
0.1
0 0.1 0 0.1 0.3 0.3 - 0 0.3
[1] 1fpk.a 0.2 0.3 0.1 0.1 0.8 0.4
0
0.1 0.4 0.2 0.1 0.2 - 0.1 0.2
[1] 1nuw.a 0.4 1.4 0.5 0.7 1.9 1.5 0
0.1
0.7 0.3 0.8 0.3 - 0.3 0.3
[1] 1nv2.a 0.7 1.2 0.2 0.1 0.5 0.5 0 0.2
0
0.3 0.5 0.2 - 0.3 0.2
[1] 1rdz.a 0.5 0.1 0.1 0 1.4 1.1 0.1 0.2 1.1
0
0.3 0.2 - 0.2 0.2
[1] 2qvu.a 0.5 1.0 0.6 0.2 1.5 1.2 0.1 0.1 0.7 0.3
0.1
0.1 - 0.3 0.4
[1] 2qvv.a 0.4 0.9 0.3 0.2 1.6 1.2 0.1 0.1 0.8 0.4 0.1
0.1
- 0.1 0.4
[1] 4fbp.a 1.8 1.4 1.2 1.0 2.0 1.5 0.2 1.1 1.7 1.4 1.5 1.4
-
1.3 1.1
[1] 4gbw.a 0.5 1.0 0.2 0.1 1.3 0.9 0.1 0.2 0.5 0.2 0.5 0.2 -
0.2
0.2
[1] 4gww.a 0.7 0.3 0.2 0 0.6 0.7 0 0.1 0.4 0.2 0.5 0.5 - 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
1fbg.a
1fbh.a
1fj6.a
1fpd.a
1fpi.a
1fpj.a
1fpk.a
1nuw.a
1nv2.a
1rdz.a
2qvu.a
2qvv.a
4fbp.a
4gbw.a
4gww.a
[1] 1fbg.a
0
.07 .11 .09 .10 .09 .05 .11 .11 .06 .11 .10 .09 .09 .09
[1] 1fbh.a .07
0
.08 .06 .10 .10 .07 .12 .13 .04 .10 .08 .08 .10 .10
[1] 1fj6.a .11 .08
0
.08 .15 .14 .09 .07 .08 .07 .04 .04 .13 .04 .13
[1] 1fpd.a .09 .06 .08
0
.08 .08 .09 .13 .14 .04 .08 .08 .10 .10 .10
[1] 1fpi.a .10 .10 .15 .08
0
.01 .07 .16 .10 .09 .11 .12 .11 .13 .05
[1] 1fpj.a .09 .10 .14 .08 .01
0
.07 .15 .09 .08 .11 .11 .10 .12 .05
[1] 1fpk.a .05 .07 .09 .09 .07 .07
0
.11 .09 .07 .09 .08 .08 .09 .05
[1] 1nuw.a .11 .12 .07 .13 .16 .15 .11
0
.08 .12 .08 .08 .14 .04 .15
[1] 1nv2.a .11 .13 .08 .14 .10 .09 .09 .08
0
.13 .11 .11 .13 .06 .10
[1] 1rdz.a .06 .04 .07 .04 .09 .08 .07 .12 .13
0
.08 .06 .09 .09 .08
[1] 2qvu.a .11 .10 .04 .08 .11 .11 .09 .08 .11 .08
0
.02 .13 .07 .13
[1] 2qvv.a .10 .08 .04 .08 .12 .11 .08 .08 .11 .06 .02
0
.11 .06 .11
[1] 4fbp.a .09 .08 .13 .10 .11 .10 .08 .14 .13 .09 .13 .11
0
.12 .09
[1] 4gbw.a .09 .10 .04 .10 .13 .12 .09 .04 .06 .09 .07 .06 .12
0
.12
[1] 4gww.a .09 .10 .13 .10 .05 .05 .05 .15 .10 .08 .13 .11 .09 .12
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 1.3 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
1fbg.a
1fbh.a
1fj6.a
1fpd.a
1fpi.a
1fpj.a
1fpk.a
1nuw.a
1nv2.a
1rdz.a
2qvu.a
2qvv.a
4fbp.a
4gbw.a
4gww.a
[1] 1fbg.a
0
0.4 1.1 0.7 0.8 0.8 0.4 1.0 1.0 0.6 1.0 1.0 0.8 0.9 0.8
[1] 1fbh.a 0.4
0
3.0 0.7 0.8 0.8 0.4 3.0 3.0 1.4 2.5 2.5 0.7 3.0 0.8
[1] 1fj6.a 1.1 3.0
0
1.1 1.1 1.2 1.2 0.2 0.3 4.2 4.6 4.5 1.1 0.2 0.8
[1] 1fpd.a 0.7 0.7 1.1
0
0.2 0.2 0.7 1.1 1.1 0.6 0.8 0.8 0.5 1.0 1.0
[1] 1fpi.a 0.8 0.8 1.1 0.2
0
0.1 0.8 1.1 1.1 0.7 0.9 0.8 0.6 1.0 1.0
[1] 1fpj.a 0.8 0.8 1.2 0.2 0.1
0
0.8 1.1 1.1 0.7 0.9 0.9 0.6 1.0 1.0
[1] 1fpk.a 0.4 0.4 1.2 0.7 0.8 0.8
0
1.2 1.2 0.6 1.1 1.1 0.8 1.1 0.9
[1] 1nuw.a 1.0 3.0 0.2 1.1 1.1 1.1 1.2
0
0.2 4.1 4.5 4.5 1.1 0.1 0.8
[1] 1nv2.a 1.0 3.0 0.3 1.1 1.1 1.1 1.2 0.2
0
4.2 4.6 4.5 1.1 0.2 0.8
[1] 1rdz.a 0.6 1.4 4.2 0.6 0.7 0.7 0.6 4.1 4.2
0
1.7 1.7 0.8 4.1 0.8
[1] 2qvu.a 1.0 2.5 4.6 0.8 0.9 0.9 1.1 4.5 4.6 1.7
0
0.1 1.0 4.5 1.0
[1] 2qvv.a 1.0 2.5 4.5 0.8 0.8 0.9 1.1 4.5 4.5 1.7 0.1
0
1.0 4.5 1.0
[1] 4fbp.a 0.8 0.7 1.1 0.5 0.6 0.6 0.8 1.1 1.1 0.8 1.0 1.0
0
1.0 1.0
[1] 4gbw.a 0.9 3.0 0.2 1.0 1.0 1.0 1.1 0.1 0.2 4.1 4.5 4.5 1.0
0
0.7
[1] 4gww.a 0.8 0.8 0.8 1.0 1.0 1.0 0.9 0.8 0.8 0.8 1.0 1.0 1.0 0.7
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 1.0 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
1fbg.a
1fbh.a
1fj6.a
1fpd.a
1fpi.a
1fpj.a
1fpk.a
1nuw.a
1nv2.a
1rdz.a
2qvu.a
2qvv.a
4fbp.a
4gbw.a
4gww.a
[1] 1fbg.a
0
0.8 1.7 1.0 1.0 1.0 0.6 1.6 1.4 0.9 1.3 1.4 1.0 1.6 1.2
[1] 1fbh.a 0.8
0
3.1 1.1 1.2 1.2 0.8 3.0 3.0 1.7 2.6 2.6 1.0 3.0 1.1
[1] 1fj6.a 1.7 3.1
0
1.7 1.8 1.8 1.7 0.8 1.0 4.5 4.7 4.6 1.8 0.7 1.4
[1] 1fpd.a 1.0 1.1 1.7
0
0.6 0.6 1.0 1.7 1.5 1.2 1.3 1.3 1.0 1.6 1.4
[1] 1fpi.a 1.0 1.2 1.8 0.6
0
0.3 1.0 1.8 1.4 1.3 1.3 1.3 0.9 1.7 1.4
[1] 1fpj.a 1.0 1.2 1.8 0.6 0.3
0
1.0 1.8 1.4 1.2 1.3 1.4 0.9 1.7 1.4
[1] 1fpk.a 0.6 0.8 1.7 1.0 1.0 1.0
0
1.7 1.4 0.9 1.3 1.4 1.0 1.6 1.2
[1] 1nuw.a 1.6 3.0 0.8 1.7 1.8 1.8 1.7
0
0.9 4.4 4.6 4.6 1.8 0.5 1.4
[1] 1nv2.a 1.4 3.0 1.0 1.5 1.4 1.4 1.4 0.9
0
4.4 4.6 4.6 1.5 0.9 1.2
[1] 1rdz.a 0.9 1.7 4.5 1.2 1.3 1.2 0.9 4.4 4.4
0
2.1 2.1 1.2 4.4 1.1
[1] 2qvu.a 1.3 2.6 4.7 1.3 1.3 1.3 1.3 4.6 4.6 2.1
0
0.4 1.3 4.6 1.4
[1] 2qvv.a 1.4 2.6 4.6 1.3 1.3 1.4 1.4 4.6 4.6 2.1 0.4
0
1.4 4.6 1.5
[1] 4fbp.a 1.0 1.0 1.8 1.0 0.9 0.9 1.0 1.8 1.5 1.2 1.3 1.4
0
1.7 1.4
[1] 4gbw.a 1.6 3.0 0.7 1.6 1.7 1.7 1.6 0.5 0.9 4.4 4.6 4.6 1.7
0
1.3
[1] 4gww.a 1.2 1.1 1.4 1.4 1.4 1.4 1.2 1.4 1.2 1.1 1.4 1.5 1.4 1.3
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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