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FABB_ECOLI_1_406

3-oxoacyl-[acyl-carrier-protein] synthase 1 [Beta-ketoacyl-ACP synthases family]

Composition of the binding site

Protein chains homodimer
A1 (FABB_ECOLI):106, 107, 110, 162, 163, 197, 200, 201, 204, 206, 229, 265, 268:272, 298, 300, 302, 305, 333, 335, 390:394106, 107, 110, 162, 163, 197, 200, 201, 204, 206, 229, 265, 268:272, 298, 300, 302, 305, 333, 335, 390:394
A2 (FABB_ECOLI):113, 133, 134, 137, 138113, 133, 134, 137, 138

Full PDB list

1dd8, 1ek4, 1f91, 1fj4, 1fj8, 1g5x, 1h4f, 2aq7, 2aqb, 2buh, 2bui, 2byw, 2byx, 2byy, 2byz, 2bz3, 2bz4, 2vb7, 2vb8, 2vb9, 2vba (redundant Pocketome entry)

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1 A2
G
1
0
6
G
1
0
7
A
1
6
2
C
1
6
3
M
1
9
7
E
2
0
0
F
2
0
1
M
2
0
4
A
2
0
6
F
2
2
9
D
2
6
8
M
2
6
9
V
2
7
0
A
2
7
1
P
2
7
2
H
2
9
8
T
3
0
0
T
3
0
2
G
3
0
5
H
3
3
3
L
3
3
5
F
3
9
0
G
3
9
1
F
3
9
2
G
3
9
3
G
3
9
4
Q
1
1
3
V
1
3
4
A
1
3
7
M
1
3
8
[1]1ek4.a dao13 . . . S . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]1f91.a dka11 . . . S . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]1fj8.a cer16 . . . * . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]2aq7.d tl515 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]2aqb.b tl613 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]2bui.b oca9 . . . * . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]2byx.a dao13 . . . * . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]2byy.a none . . . . . . . . . . . . . . . E . . . . . . . . . . . . . .
[1]2byz.d dao13 . . . * . . . . . . . . . . . Q . . . . . . . . . . . . . .
[1]2bz3.a dao13 . . . * . . . . . . . . . . . E . . . . . . . . . . . . . .
[1]2bz4.a none . . . . . . . . . . . . . . . Q . . . . . . . . . . . . . .
[1]2vb7.c none . . . * . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]2vb8.b tlm14 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]2vb9.a none . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]2vba.a p4t16 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

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
G
1
0
6
G
1
0
7
P
1
1
0
A
1
6
2
C
1
6
3
M
1
9
7
E
2
0
0
F
2
0
1
M
2
0
4
A
2
0
6
F
2
2
9
D
2
6
5
D
2
6
8
M
2
6
9
V
2
7
0
A
2
7
1
P
2
7
2
H
2
9
8
T
3
0
0
T
3
0
2
G
3
0
5
H
3
3
3
L
3
3
5
F
3
9
0
G
3
9
1
F
3
9
2
G
3
9
3
G
3
9
4
Q
1
1
3
V
1
3
3
V
1
3
4
A
1
3
7
M
1
3
8
[1]1ek4.a . . . . S . . . . . . . . . . . . . . . . . . . . * . . . . . . .
[1]1f91.a . . . . S . * . . . . . . . . . . . . . . . . . . * . . . . . . .
[1]1fj8.a . . . . * . . . . . . . . . . . . . . . . . . . . * . . . . . . .
[1]2aq7.d . . . . * . * . . . . . . . . . . . . . . . . . . * . . . . . . .
[1]2aqb.b . . . . * . * . . . . . . . . . . . . . . . . . . * . . . . . . .
[1]2bui.b . . . . * . * . . . . . . . . . . . . . . . . . . * . . . . . . .
[1]2byx.a . . . . * . . . . . . . . . . . . . . . . . . . . * . . . . . . .
[1]2byy.a . . . . * . * . . . . . . . . . . E . . . . . . . * . . . . . . .
[1]2byz.d . . . . * . * . . . . . . . . . . Q . . . . . * . * . . . . . . .
[1]2bz3.a . . . . * . . . . . . . . . . . . E . . . . . . . * . . . . . . .
[1]2bz4.a . . . . * . * . . . . . . . . . . Q . . . . . . . * . . . . . . .
[1]2vb7.c . . . . csw . * . . . . . . . . . . . . . . . . . . * . . . . . . .
[1]2vb8.b . . . . * . * . . . . . . . . . . . . . . . . . . * . . . . . . .
[1]2vb9.a . . . . * . * . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]2vba.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
1ek4.a:dao
1f91.a:dka
1fj8.a:cer
2aq7.d:tl5
2aqb.b:tl6
2bui.b:oca
2byx.a:dao
2byy.a is apo
2byz.d:dao
2bz3.a:dao
2bz4.a is apo
2vb7.c is apo
2vb8.b:tlm
2vb9.a is apo
2vba.a:p4t
[1] 1ek4.a
0.6
0.8 0.5 0.5 0.4 0.4 0.3 - 0.4 0.4 - - 0.5 - 1.2
[1] 1f91.a 1.1
0.6
0.9 0.5 0.3 0.3 0.6 - 0.5 1.2 - - 0.3 - 1.2
[1] 1fj8.a 1.4 0.7
0.4
0.3 0.1 0.4 0.8 - 0.5 0.8 - - 0.1 - 1.2
[1] 2aq7.d 2.1 1.3 1.6
0.3
0 0.6 2.2 - 1.1 2.2 - - 0.3 - 1.9
[1] 2aqb.b 1.6 1.1 1.3 0.4
0.1
0.7 1.4 - 0.7 1.5 - - 0.3 - 1.8
[1] 2bui.b 1.6 0.9 0.9 0.3 0.2
0.4
1.3 - 0.8 1.7 - - 0.3 - 1.6
[1] 2byx.a 0.8 0.9 0.5 0.3 0.1 0.6
0.4
- 0.6 0.6 - - 0.1 - 1.4
[1] 2byy.a 1.4 0.9 1.2 0.5 0.4 0.6 1.1
-
0.8 1.5 - - 0.4 - 1.7
[1] 2byz.d 1.0 0.6 0.4 3.1 1.6 0.4 0.7 -
0.4
1.2 - - 2.7 - 1.4
[1] 2bz3.a 0.8 0.9 0.3 0.6 0.3 0.4 0.4 - 0.7
0.4
- - 0.4 - 1.4
[1] 2bz4.a 2.2 1.4 2.0 0.6 0.8 1.2 2.1 - 1.6 2.3
-
- 0.6 - 2.7
[1] 2vb7.c 2.8 1.9 2.4 0.8 0.4 1.4 2.6 - 2.2 3.0 -
-
0.7 - 2.4
[1] 2vb8.b 2.2 1.0 1.5 0.1 0 0.6 2.2 - 1.1 2.0 - -
0
- 1.7
[1] 2vb9.a 1.4 0.8 1.1 0.2 0.2 0.6 1.5 - 0.8 1.6 - - 0.7
-
0.3
[1] 2vba.a 1.6 0.8 0.8 0.2 0.2 0.6 1.6 - 1.0 1.7 - - 0.5 -
0
[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
1ek4.a
1f91.a
1fj8.a
2aq7.d
2aqb.b
2bui.b
2byx.a
2byy.a
2byz.d
2bz3.a
2bz4.a
2vb7.c
2vb8.b
2vb9.a
2vba.a
[1] 1ek4.a
0
.06 .04 .11 .08 .06 .02 .07 .12 .03 .14 .11 .09 .10 .10
[1] 1f91.a .06
0
.05 .07 .05 .04 .06 .04 .10 .06 .08 .08 .06 .05 .06
[1] 1fj8.a .04 .05
0
.09 .06 .05 .03 .05 .13 .04 .12 .11 .06 .08 .07
[1] 2aq7.d .11 .07 .09
0
.07 .07 .10 .08 .17 .11 .10 .08 .03 .09 .08
[1] 2aqb.b .08 .05 .06 .07
0
.03 .07 .05 .14 .08 .07 .07 .07 .08 .08
[1] 2bui.b .06 .04 .05 .07 .03
0
.05 .02 .12 .05 .10 .08 .05 .08 .08
[1] 2byx.a .02 .06 .03 .10 .07 .05
0
.06 .13 .02 .13 .12 .07 .10 .09
[1] 2byy.a .07 .04 .05 .08 .05 .02 .06
0
.13 .05 .09 .09 .06 .09 .10
[1] 2byz.d .12 .10 .13 .17 .14 .12 .13 .13
0
.13 .17 .16 .15 .13 .15
[1] 2bz3.a .03 .06 .04 .11 .08 .05 .02 .05 .13
0
.11 .12 .08 .10 .10
[1] 2bz4.a .14 .08 .12 .10 .07 .10 .13 .09 .17 .11
0
.10 .10 .09 .10
[1] 2vb7.c .11 .08 .11 .08 .07 .08 .12 .09 .16 .12 .10
0
.09 .10 .11
[1] 2vb8.b .09 .06 .06 .03 .07 .05 .07 .06 .15 .08 .10 .09
0
.08 .08
[1] 2vb9.a .10 .05 .08 .09 .08 .08 .10 .09 .13 .10 .09 .10 .08
0
.02
[1] 2vba.a .10 .06 .07 .08 .08 .08 .09 .10 .15 .10 .10 .11 .08 .02
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 0.8 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
1ek4.a
1f91.a
1fj8.a
2aq7.d
2aqb.b
2bui.b
2byx.a
2byy.a
2byz.d
2bz3.a
2bz4.a
2vb7.c
2vb8.b
2vb9.a
2vba.a
[1] 1ek4.a
0
0.2 0.5 0.4 0.4 0.3 0.3 0.3 0.2 0.3 0.5 0.3 0.4 0.8 0.7
[1] 1f91.a 0.2
0
0.5 0.4 0.3 0.3 0.3 0.3 0.3 0.3 0.4 0.3 0.4 0.8 0.6
[1] 1fj8.a 0.5 0.5
0
0.5 0.5 0.4 0.4 0.5 0.5 0.4 0.6 0.5 0.4 0.9 0.8
[1] 2aq7.d 0.4 0.4 0.5
0
0.3 0.4 0.4 0.4 0.4 0.4 0.4 0.4 0.3 0.6 0.5
[1] 2aqb.b 0.4 0.3 0.5 0.3
0
0.2 0.3 0.3 0.4 0.3 0.3 0.2 0.3 0.7 0.6
[1] 2bui.b 0.3 0.3 0.4 0.4 0.2
0
0.2 0.2 0.3 0.2 0.4 0.3 0.3 0.8 0.7
[1] 2byx.a 0.3 0.3 0.4 0.4 0.3 0.2
0
0.3 0.2 0.2 0.5 0.4 0.3 0.8 0.7
[1] 2byy.a 0.3 0.3 0.5 0.4 0.3 0.2 0.3
0
0.3 0.2 0.4 0.3 0.3 0.8 0.7
[1] 2byz.d 0.2 0.3 0.5 0.4 0.4 0.3 0.2 0.3
0
0.2 0.5 0.3 0.3 0.8 0.7
[1] 2bz3.a 0.3 0.3 0.4 0.4 0.3 0.2 0.2 0.2 0.2
0
0.4 0.3 0.3 0.8 0.7
[1] 2bz4.a 0.5 0.4 0.6 0.4 0.3 0.4 0.5 0.4 0.5 0.4
0
0.3 0.5 0.6 0.6
[1] 2vb7.c 0.3 0.3 0.5 0.4 0.2 0.3 0.4 0.3 0.3 0.3 0.3
0
0.4 0.7 0.6
[1] 2vb8.b 0.4 0.4 0.4 0.3 0.3 0.3 0.3 0.3 0.3 0.3 0.5 0.4
0
0.8 0.7
[1] 2vb9.a 0.8 0.8 0.9 0.6 0.7 0.8 0.8 0.8 0.8 0.8 0.6 0.7 0.8
0
0.3
[1] 2vba.a 0.7 0.6 0.8 0.5 0.6 0.7 0.7 0.7 0.7 0.7 0.6 0.6 0.7 0.3
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 0.4 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
1ek4.a
1f91.a
1fj8.a
2aq7.d
2aqb.b
2bui.b
2byx.a
2byy.a
2byz.d
2bz3.a
2bz4.a
2vb7.c
2vb8.b
2vb9.a
2vba.a
[1] 1ek4.a
0
0.3 0.9 1.0 0.8 0.6 0.7 0.6 1.1 0.7 0.8 0.7 0.9 1.1 1.0
[1] 1f91.a 0.3
0
0.9 0.9 0.7 0.6 0.7 0.5 1.1 0.7 0.7 0.7 0.9 1.0 0.9
[1] 1fj8.a 0.9 0.9
0
0.6 0.7 0.7 0.7 0.8 1.1 0.6 0.9 0.8 0.7 1.2 1.1
[1] 2aq7.d 1.0 0.9 0.6
0
0.6 0.8 0.8 0.9 1.3 0.8 0.9 0.8 0.7 1.1 1.0
[1] 2aqb.b 0.8 0.7 0.7 0.6
0
0.6 0.9 0.7 1.1 0.8 0.8 0.7 0.8 1.0 0.9
[1] 2bui.b 0.6 0.6 0.7 0.8 0.6
0
0.7 0.5 1.1 0.7 0.8 0.6 0.8 1.1 1.0
[1] 2byx.a 0.7 0.7 0.7 0.8 0.9 0.7
0
0.7 1.1 0.6 0.8 0.8 0.7 1.2 1.1
[1] 2byy.a 0.6 0.5 0.8 0.9 0.7 0.5 0.7
0
1.1 0.6 0.6 0.6 0.8 1.0 0.9
[1] 2byz.d 1.1 1.1 1.1 1.3 1.1 1.1 1.1 1.1
0
1.1 1.2 1.1 1.1 1.4 1.4
[1] 2bz3.a 0.7 0.7 0.6 0.8 0.8 0.7 0.6 0.6 1.1
0
0.7 0.7 0.7 1.1 1.1
[1] 2bz4.a 0.8 0.7 0.9 0.9 0.8 0.8 0.8 0.6 1.2 0.7
0
0.6 0.8 1.1 1.0
[1] 2vb7.c 0.7 0.7 0.8 0.8 0.7 0.6 0.8 0.6 1.1 0.7 0.6
0
0.6 0.9 0.8
[1] 2vb8.b 0.9 0.9 0.7 0.7 0.8 0.8 0.7 0.8 1.1 0.7 0.8 0.6
0
1.1 1.0
[1] 2vb9.a 1.1 1.0 1.2 1.1 1.0 1.1 1.2 1.0 1.4 1.1 1.1 0.9 1.1
0
0.4
[1] 2vba.a 1.0 0.9 1.1 1.0 0.9 1.0 1.1 0.9 1.4 1.1 1.0 0.8 1.0 0.4
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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