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FABF_ECOLI_1_413

3-oxoacyl-[acyl-carrier-protein] synthase 2 [Beta-ketoacyl-ACP synthases family]

Composition of the binding site

Protein chains monomer
A1 (FABF_ECOLI):108, 109, 112, 163, 164, 192, 194, 199, 203, 206:208, 230, 269, 271:273, 304, 306, 308:311, 341, 343, 399:401108, 109, 112, 163, 164, 192, 194, 199, 203, 206:208, 230, 269, 271:273, 304, 306, 308:311, 341, 343, 399:401

Full PDB list

1b3n, 1kas, 2gfv, 2gfw, 2gfx, 2gfy, 3g0y, 3g11, 3hnz, 3ho2, 3ho9, 3i8p (redundant Pocketome entry)

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1
G
1
0
8
I
1
0
9
L
1
1
2
A
1
6
3
C
1
6
4
E
1
9
2
A
1
9
4
G
1
9
9
F
2
0
3
A
2
0
6
R
2
0
7
A
2
0
8
H
2
6
9
T
2
7
1
S
2
7
2
P
2
7
3
H
3
0
4
T
3
0
6
T
3
0
8
P
3
0
9
A
3
1
0
G
3
1
1
H
3
4
1
L
3
4
3
F
3
9
9
G
4
0
0
F
4
0
1
[1]1b3n.a cer16 . . . . * . . . . . . . . . . . . . . . . . . . . . .
[1]2gfv.a none . . . . Q . . . . . . . . . . . . . . . . . . . . . .
[1]2gfw.a none . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]2gfx.a pmn32 . . . . Q . . . . . . . . . . . . . . . . . . . . . .
[1]2gfy.a dao13 . . . . * . . . . . . . . . . . . . . . . . . . . . .
[1]3g0y.a p9a32 . . . . Q . . . . . . . . . . . . . . . . . . . . . .
[1]3g11.a p9c38 . . . . Q . . . . . . . . . . . . . . . . . . . . . .
[1]3hnz.a pmn32 . . . . A . . . . . . . . . . . . . . . . . . . . . .
[1]3ho2.a n3231 . . . . A . . . . . . . . . . . . . . . . . . . . . .
[1]3ho9.a n3a32 . . . . A . . . . . . . . . . . . . . . . . . . . . .
[1]3i8p.a 84033 . . . . A . . . . . . . . . . . . . . . . . . . . . .

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
G
1
0
8
I
1
0
9
L
1
1
2
A
1
6
3
C
1
6
4
E
1
9
2
A
1
9
4
G
1
9
9
F
2
0
3
A
2
0
6
R
2
0
7
A
2
0
8
F
2
3
0
H
2
6
9
T
2
7
1
S
2
7
2
P
2
7
3
H
3
0
4
T
3
0
6
T
3
0
8
P
3
0
9
A
3
1
0
G
3
1
1
H
3
4
1
L
3
4
3
F
3
9
9
G
4
0
0
F
4
0
1
[1]1b3n.a . . . . * . . . . . . . . . . . . . . . . . . . . . . .
[1]2gfv.a . * . . Q . . . . . . . . . . . . . . . . . . . . . . .
[1]2gfw.a . * . . * . . . . . . . . . . . . . . . . . . . . . . *
[1]2gfx.a . * . . Q . . . . . . . . . . . . . . . . . . . . . . .
[1]2gfy.a . . . . * . . . . . . . . . . . . . . . . . . . . . . .
[1]3g0y.a . * . . Q . . . . . . . . . . . . . . . . . . . . . . .
[1]3g11.a . * . . Q . . . . . . . . . . . . . . . . . . . . . . .
[1]3hnz.a . * . . A . . . . . . . . . . . . . . . . . . . . . . .
[1]3ho2.a . * . . A . . . . . . . . . . . . . . . . . . . . . . .
[1]3ho9.a . * . . A . . . . . . . . . . . . . . . . . . . . . . .
[1]3i8p.a . * . . 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
1b3n.a:cer
2gfv.a is apo
2gfw.a is apo
2gfx.a:pmn
2gfy.a:dao
3g0y.a:p9a
3g11.a:p9c
3hnz.a:pmn
3ho2.a:n32
3ho9.a:n3a
3i8p.a:840
[1] 1b3n.a
0.4
- - 0.2 0.4 0.1 0.1 0.1 0.2 0.2 0.2
[1] 2gfv.a 4.6
-
- 0.2 4.5 0.3 0.2 0.3 0.4 0.3 0.2
[1] 2gfw.a 4.5 -
-
0.5 3.3 0.6 0.6 0.7 0.9 0.9 0.9
[1] 2gfx.a 4.6 - -
0.1
4.7 0 0 0.3 0.2 0.2 0.2
[1] 2gfy.a 0.8 - - 0.5
0.6
0.4 0.4 0.4 0.3 0.3 0.3
[1] 3g0y.a 4.7 - - 0 4.7
0
0.1 0.3 0.3 0.2 0.3
[1] 3g11.a 4.3 - - 0.1 4.5 0.1
0
0.3 0.2 0.2 0.2
[1] 3hnz.a 2.7 - - 0.1 1.9 0.1 0.1
0.1
0.2 0.2 0.2
[1] 3ho2.a 1.9 - - 0.1 1.9 0.1 0.1 0
0
0 0.1
[1] 3ho9.a 1.9 - - 0.1 2.1 0.1 0.2 0 0
0
0
[1] 3i8p.a 1.9 - - 0.1 2.1 0.1 0.2 0 0 0
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
1b3n.a
2gfv.a
2gfw.a
2gfx.a
2gfy.a
3g0y.a
3g11.a
3hnz.a
3ho2.a
3ho9.a
3i8p.a
[1] 1b3n.a
0
.16 .17 .17 .03 .17 .15 .12 .10 .10 .10
[1] 2gfv.a .16
0
.17 .04 .16 .05 .03 .14 .14 .14 .14
[1] 2gfw.a .17 .17
0
.17 .15 .18 .17 .12 .12 .11 .11
[1] 2gfx.a .17 .04 .17
0
.17 .02 .02 .13 .12 .11 .12
[1] 2gfy.a .03 .16 .15 .17
0
.18 .16 .13 .11 .11 .12
[1] 3g0y.a .17 .05 .18 .02 .18
0
.02 .13 .12 .11 .11
[1] 3g11.a .15 .03 .17 .02 .16 .02
0
.14 .11 .11 .12
[1] 3hnz.a .12 .14 .12 .13 .13 .13 .14
0
.04 .04 .04
[1] 3ho2.a .10 .14 .12 .12 .11 .12 .11 .04
0
.01 .01
[1] 3ho9.a .10 .14 .11 .11 .11 .11 .11 .04 .01
0
0
[1] 3i8p.a .10 .14 .11 .12 .12 .11 .12 .04 .01 0
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 0.7 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
1b3n.a
2gfv.a
2gfw.a
2gfx.a
2gfy.a
3g0y.a
3g11.a
3hnz.a
3ho2.a
3ho9.a
3i8p.a
[1] 1b3n.a
0
0.3 0.5 0.4 0.3 0.4 0.4 0.5 0.4 0.4 0.5
[1] 2gfv.a 0.3
0
0.4 0.3 0.4 0.3 0.3 0.4 0.3 0.3 0.4
[1] 2gfw.a 0.5 0.4
0
0.5 0.5 0.5 0.5 0.5 0.5 0.4 0.5
[1] 2gfx.a 0.4 0.3 0.5
0
0.4 0.1 0.2 0.2 0.2 0.2 0.2
[1] 2gfy.a 0.3 0.4 0.5 0.4
0
0.4 0.4 0.5 0.4 0.4 0.5
[1] 3g0y.a 0.4 0.3 0.5 0.1 0.4
0
0.1 0.3 0.2 0.2 0.2
[1] 3g11.a 0.4 0.3 0.5 0.2 0.4 0.1
0
0.3 0.2 0.2 0.2
[1] 3hnz.a 0.5 0.4 0.5 0.2 0.5 0.3 0.3
0
0.2 0.2 0.2
[1] 3ho2.a 0.4 0.3 0.5 0.2 0.4 0.2 0.2 0.2
0
0.1 0.1
[1] 3ho9.a 0.4 0.3 0.4 0.2 0.4 0.2 0.2 0.2 0.1
0
0.1
[1] 3i8p.a 0.5 0.4 0.5 0.2 0.5 0.2 0.2 0.2 0.1 0.1
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 0.3 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
1b3n.a
2gfv.a
2gfw.a
2gfx.a
2gfy.a
3g0y.a
3g11.a
3hnz.a
3ho2.a
3ho9.a
3i8p.a
[1] 1b3n.a
0
0.8 1.0 0.9 0.7 1.0 1.1 0.9 1.0 1.0 1.1
[1] 2gfv.a 0.8
0
0.6 0.4 0.7 0.7 0.7 0.5 0.7 0.7 0.7
[1] 2gfw.a 1.0 0.6
0
0.7 0.9 0.8 0.8 0.7 0.8 0.7 0.8
[1] 2gfx.a 0.9 0.4 0.7
0
0.7 0.6 0.7 0.3 0.7 0.7 0.7
[1] 2gfy.a 0.7 0.7 0.9 0.7
0
1.0 1.1 0.8 1.0 1.0 1.0
[1] 3g0y.a 1.0 0.7 0.8 0.6 1.0
0
0.2 0.7 0.3 0.3 0.3
[1] 3g11.a 1.1 0.7 0.8 0.7 1.1 0.2
0
0.8 0.2 0.3 0.3
[1] 3hnz.a 0.9 0.5 0.7 0.3 0.8 0.7 0.8
0
0.7 0.7 0.7
[1] 3ho2.a 1.0 0.7 0.8 0.7 1.0 0.3 0.2 0.7
0
0.2 0.1
[1] 3ho9.a 1.0 0.7 0.7 0.7 1.0 0.3 0.3 0.7 0.2
0
0.2
[1] 3i8p.a 1.1 0.7 0.8 0.7 1.0 0.3 0.3 0.7 0.1 0.2
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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