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ALF_MYCTU_1_344

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

Composition of the binding site

Protein chains homodimer [domain annotation]
A1 (ALF_MYCTU):R: Dihydroxyacetone phosphate binding (253:255)
R: Dihydroxyacetone phosphate binding (274:277)
27, 51, 53, 55, 95, 96, 169, 170, 212, 213, 252
27, 51, 53, 55, 95, 96, 169, 170, 212, 213, 252:255, 274:277
A2 (ALF_MYCTU):314314
Metals (Me):Na/Zn

Full PDB list

3ekl, 3ekz, 3elf, 4a21, 4a22, 4def, 4del, 4lv4 (redundant Pocketome entry)

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1 A2 Me
N
2
7
Q
5
1
S
5
3
G
5
5
D
9
5
H
9
6
H
2
1
2
G
2
1
3
H
2
5
2
G
2
5
3
G
2
5
4
S
2
5
5
N
2
7
4
V
2
7
5
D
2
7
6
T
2
7
7
R
3
1
4
[1]3ekl.a 13p,13p20 . . . . . . . . . . . . . . . . . Na,Zn
[1]3ekz.a 13p,13p,g3p30 . . . . . . . . . . . . . . . . . Na,Zn
[1]3elf.a 2fp20 . . . . . . . . . . . . . . . . . Na,Zn
[1]4a22.a td419 . . . . . . . . . . . . . . . . . Na,Zn
[1]4a22.b so4,so4,td429 . . . . . . . . . . . . . . . . . Na,Zn
[1]4def.a none . . . . . . . . . . . . . . . . . Na,Zn
[1]4del.a pgh10 . . . . . . . . . . . . . . . . . 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
7
Q
5
1
S
5
3
G
5
5
D
9
5
H
9
6
E
1
6
9
D
1
7
0
H
2
1
2
G
2
1
3
H
2
5
2
G
2
5
3
G
2
5
4
S
2
5
5
N
2
7
4
V
2
7
5
D
2
7
6
T
2
7
7
R
3
1
4
[1]3ekl.a . . . . . . - - . . . . . . . . . . . Na,Zn
[1]3ekz.a . . . . . . - - . . . . . . . . . . . Na,Zn
[1]3elf.a . . . . . . - - . . . . . . . . . . . Na,Zn
[1]4a22.a . . . . . . - - . . . . . . . . . . . Na,Zn
[1]4a22.b . . . . . . - - . . . . . . . . . . . Na,Zn
[1]4def.a . . . . . . - - . . . . . . . . . . . Na,Zn
[1]4del.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
3ekl.a:13p
3ekz.a:13p,g3p
3elf.a:2fp
4a22.a:td4
4a22.b:so4,td4
4def.a is apo
4del.a:pgh
[1] 3ekl.a
0.3
0.4 0.5 0.2 0.3 - 0.2
[1] 3ekz.a 0.3
0.2
0.2 0.2 0.5 - 0
[1] 3elf.a 0.3 0.4
0.1
0.2 0.5 - 0
[1] 4a22.a 0.3 0.4 0.6
0.2
0.4 - 0
[1] 4a22.b 0.3 0.3 0.3 0.2
0.3
- 0.1
[1] 4def.a 0.2 0.3 0.6 0.2 0.2
-
0.1
[1] 4del.a 0.3 1.2 1.2 2.0 1.7 -
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
3ekl.a
3ekz.a
3elf.a
4a22.a
4a22.b
4def.a
4del.a
[1] 3ekl.a
0
.02 .03 .02 .03 .02 .11
[1] 3ekz.a .02
0
.01 .02 .03 .03 .11
[1] 3elf.a .03 .01
0
.03 .03 .04 .12
[1] 4a22.a .02 .02 .03
0
.03 .01 .11
[1] 4a22.b .03 .03 .03 .03
0
.03 .10
[1] 4def.a .02 .03 .04 .01 .03
0
.11
[1] 4del.a .11 .11 .12 .11 .10 .11
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 0.3 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
3ekl.a
3ekz.a
3elf.a
4a22.a
4a22.b
4def.a
4del.a
[1] 3ekl.a
0
0.1 0.2 0.1 0.2 0.3 0.1
[1] 3ekz.a 0.1
0
0.1 0.2 0.2 0.3 0.1
[1] 3elf.a 0.2 0.1
0
0.2 0.2 0.3 0.2
[1] 4a22.a 0.1 0.2 0.2
0
0.2 0.3 0.2
[1] 4a22.b 0.2 0.2 0.2 0.2
0
0.2 0.2
[1] 4def.a 0.3 0.3 0.3 0.3 0.2
0
0.3
[1] 4del.a 0.1 0.1 0.2 0.2 0.2 0.3
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

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
3ekl.a
3ekz.a
3elf.a
4a22.a
4a22.b
4def.a
4del.a
[1] 3ekl.a
0
0.2 0.3 0.5 0.5 0.3 0.2
[1] 3ekz.a 0.2
0
0.2 0.5 0.6 0.4 0.3
[1] 3elf.a 0.3 0.2
0
0.5 0.6 0.4 0.3
[1] 4a22.a 0.5 0.5 0.5
0
0.3 0.5 0.5
[1] 4a22.b 0.5 0.6 0.6 0.3
0
0.5 0.5
[1] 4def.a 0.3 0.4 0.4 0.5 0.5
0
0.3
[1] 4del.a 0.2 0.3 0.3 0.5 0.5 0.3
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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