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ALF_THECA_1_305

Fructose-bisphosphate aldolase [Class II fructose-bisphosphate aldolase family]

Composition of the binding site

Protein chains monomer [domain annotation]
A1 (ALF_THECA):R: Dihydroxyacetone phosphate binding (209:211)
R: Dihydroxyacetone phosphate binding (251:254)
23, 80, 81, 136, 178, 179, 182, 208
23, 80, 81, 136, 178, 179, 182, 208:211, 251:254
Metals (Me):Co/Na

Full PDB list

1rv8, 1rvg, 2fjk

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1 Me
D
8
0
H
8
1
H
1
7
8
K
1
8
2
H
2
0
8
G
2
0
9
A
2
1
0
S
2
1
1
N
2
5
1
T
2
5
2
D
2
5
3
T
2
5
4
[1]1rv8.a co1 . . . . . . . . . . . . Na
[1]1rvg.b none . . . . . . . . . . . . Co,Na
[1]2fjk.d 13p10 . . . . . . . . . . . .

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
N
2
3
D
8
0
H
8
1
L
1
3
6
H
1
7
8
G
1
7
9
K
1
8
2
H
2
0
8
G
2
0
9
A
2
1
0
S
2
1
1
N
2
5
1
T
2
5
2
D
2
5
3
T
2
5
4
[1]1rv8.a . . . . . . . . . . . . . . . Na
[1]1rvg.b . . . . . . . . . . . . . . . Co,Na
[1]2fjk.d . . . . . . . . . . . . . . .

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
1rv8.a:co
1rvg.b is apo
2fjk.d:13p
[1] 1rv8.a
0.4
- 0.9
[1] 1rvg.b 0.3
-
0.2
[1] 2fjk.d 0.3 -
0.4
[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
1rv8.a
1rvg.b
2fjk.d
[1] 1rv8.a
0
.04 .03
[1] 1rvg.b .04
0
.01
[1] 2fjk.d .03 .01
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
1rv8.a
1rvg.b
2fjk.d
[1] 1rv8.a
0
5.1 0.7
[1] 1rvg.b 5.1
0
5.2
[1] 2fjk.d 0.7 5.2
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 0.7 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
1rv8.a
1rvg.b
2fjk.d
[1] 1rv8.a
0
5.3 1.0
[1] 1rvg.b 5.3
0
5.5
[1] 2fjk.d 1.0 5.5
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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