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ALDOB_HUMAN_2_364

Fructose-bisphosphate aldolase B [Class I fructose-bisphosphate aldolase family]

Composition of the binding site

Protein chains monomer
A1 (ALDOB_HUMAN):32, 34, 35, 39, 43, 108, 147, 149, 188, 190, 230, 271:274, 301:304, 363, 36432, 34, 35, 39, 43, 108, 147, 149, 188, 190, 230, 271:274, 301:304, 363, 364

Full PDB list

1fdj, 1xdl, 1xdm (redundant Pocketome entry)

Pocket contact map

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PDB.ch
   
ligand
A1
A
3
2
D
3
4
E
3
5
T
3
9
R
4
3
K
1
0
8
K
1
4
7
R
1
4
9
E
1
8
8
E
1
9
0
K
2
3
0
L
2
7
1
S
2
7
2
G
2
7
3
G
2
7
4
S
3
0
1
Y
3
0
2
G
3
0
3
R
3
0
4
[1]1fdj.a 2fp20 . . . . . . . . . . . . . . . . . . .
[1]1fdj.b 13p,2fp,g3p40 . . . . . . . . . . . . . . . . . . .
[1]1fdj.c 13p10 . . . . . . . . . . . . . . . . . . .
[1]1fdj.d 13p,13p20 . . . . . . . . . . . . . . . . . . .
[2]1xdl.a none . . . . . . . . . . . . . . . . . . .

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

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PDB.ch
A1
A
3
2
D
3
4
E
3
5
T
3
9
R
4
3
K
1
0
8
K
1
4
7
R
1
4
9
E
1
8
8
E
1
9
0
K
2
3
0
L
2
7
1
S
2
7
2
G
2
7
3
G
2
7
4
S
3
0
1
Y
3
0
2
G
3
0
3
R
3
0
4
T
3
6
3
Y
3
6
4
[1]1fdj.a . . . . . . . . . . . . . . . . . . . . .
[1]1fdj.b . . . . . . . . . . . . . . . . . . . . .
[1]1fdj.c . . . . . . . . . . . . . . . . . . . . *
[1]1fdj.d . . . . . . . . . . . . . . . . . . . . *
[2]1xdl.a . . . . . . . . . . . . . . . . . . * - -

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
1fdj.a:2fp
1fdj.b:13p,2fp,g3p
1fdj.c:13p
1fdj.d:13p
1xdl.a is apo
[1] 1fdj.a
0
1.0 0.1 0.2 -
[1] 1fdj.b 0.1
0
0.2 0 -
[1] 1fdj.c 0.1 2.8
0
0.1 -
[1] 1fdj.d 0.8 4.7 0.2
0.1
-
[2] 1xdl.a 3.5 4.9 4.1 4.1
-
[Pocket-ligand steric clashes matrix]

Pocket clash dissimilarity (2 clusters)

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
1fdj.a
1fdj.b
1fdj.c
1fdj.d
1xdl.a
[1] 1fdj.a
0
.06 .13 .20 .23
[1] 1fdj.b .06
0
.15 .22 .23
[1] 1fdj.c .13 .15
0
.11 .31
[1] 1fdj.d .20 .22 .11
0
.35
[2] 1xdl.a .23 .23 .31 .35
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 1.8 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
1fdj.a
1fdj.b
1fdj.c
1fdj.d
1xdl.a
[1] 1fdj.a
0
11 12 13 0.6
[1] 1fdj.b 11
0
2.1 3.1 0.6
[1] 1fdj.c 12 2.1
0
2.1 0.6
[1] 1fdj.d 13 3.1 2.1
0
0.6
[2] 1xdl.a 0.6 0.6 0.6 0.6
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 0.6 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
1fdj.a
1fdj.b
1fdj.c
1fdj.d
1xdl.a
[1] 1fdj.a
0
13 14 14 1.5
[1] 1fdj.b 13
0
2.9 3.4 1.8
[1] 1fdj.c 14 2.9
0
2.2 1.7
[1] 1fdj.d 14 3.4 2.2
0
1.3
[2] 1xdl.a 1.5 1.8 1.7 1.3
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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