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ALF_HELPY_1_307

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

Composition of the binding site

Protein chains homodimer [domain annotation]
A1 (ALF_HELPY):R: Dihydroxyacetone phosphate binding (211:213)
R: Dihydroxyacetone phosphate binding (253:256)
23, 47, 49, 82, 83, 180, 181, 184, 210, 259
23, 47, 49, 82, 83, 180, 181, 184, 210:213, 253:256, 259
A2 (ALF_HELPY):280280
Metals (Me):Na/Zn

Full PDB list

3c4u, 3c52, 3c56, 3n9r, 3n9s

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1 A2 Me
N
2
3
S
4
9
D
8
2
H
8
3
H
1
8
0
G
1
8
1
K
1
8
4
H
2
1
0
G
2
1
1
A
2
1
2
S
2
1
3
N
2
5
3
D
2
5
5
T
2
5
6
R
2
5
9
R
2
8
0
[1]3c4u.b none . . . . . . . . . . . . . . . . Na
[1]3c52.b pgh10 . . . . . . . . . . . . . . . . Na,Zn
[1]3c56.a ph418 . . . . . . . . . . . . . . . . Zn
[1]3n9r.a td315 . . . . . . . . . . . . . . . . Na,Zn
[1]3n9s.a td419 . . . . . . . . . . . . . . . . Na,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 A2 Me
N
2
3
Q
4
7
S
4
9
D
8
2
H
8
3
H
1
8
0
G
1
8
1
K
1
8
4
H
2
1
0
G
2
1
1
A
2
1
2
S
2
1
3
N
2
5
3
T
2
5
4
D
2
5
5
T
2
5
6
R
2
5
9
R
2
8
0
[1]3c4u.b . . . . . . . . . . . . . . . . . . Na
[1]3c52.b . . . . . . . . . . . . . . . . . . Na,Zn
[1]3c56.a . . . . . . . . . . . . . . . . . . Zn
[1]3n9r.a . . . . . . . . . . . . . . . . . . Na,Zn
[1]3n9s.a . . . . . . . . . . . . . . . . . . Na,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
3c4u.b is apo
3c52.b:pgh
3c56.a:ph4
3n9r.a:td3
3n9s.a:td4
[1] 3c4u.b
-
0.2 0.3 0.3 0.2
[1] 3c52.b -
0.5
0.4 0.4 0.3
[1] 3c56.a - 0.4
0.3
0.1 0.5
[1] 3n9r.a - 0.4 0.2
0.1
0.2
[1] 3n9s.a - 0.4 0.3 0.3
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
3c4u.b
3c52.b
3c56.a
3n9r.a
3n9s.a
[1] 3c4u.b
0
.03 .04 .04 .04
[1] 3c52.b .03
0
.03 .03 .02
[1] 3c56.a .04 .03
0
.02 .03
[1] 3n9r.a .04 .03 .02
0
.02
[1] 3n9s.a .04 .02 .03 .02
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 0.5 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
3c4u.b
3c52.b
3c56.a
3n9r.a
3n9s.a
[1] 3c4u.b
0
3.8 3.9 3.8 3.9
[1] 3c52.b 3.8
0
0.2 0.2 0.2
[1] 3c56.a 3.9 0.2
0
0.3 0.2
[1] 3n9r.a 3.8 0.2 0.3
0
0.2
[1] 3n9s.a 3.9 0.2 0.2 0.2
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 0.2 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
3c4u.b
3c52.b
3c56.a
3n9r.a
3n9s.a
[1] 3c4u.b
0
3.5 3.5 3.5 3.6
[1] 3c52.b 3.5
0
0.5 0.5 0.5
[1] 3c56.a 3.5 0.5
0
0.5 0.6
[1] 3n9r.a 3.5 0.5 0.5
0
0.6
[1] 3n9s.a 3.6 0.5 0.6 0.6
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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