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FABA_PSEAE_1_171

3-hydroxydecanoyl-[acyl-carrier-protein] dehydratase [Thioester dehydratase family. FabA subfamily]

Composition of the binding site

Protein chains homodimer
A1 (FABA_PSEAE):15, 26:28, 84, 87, 88, 91, 92, 103:106, 161, 162, 165, 17115, 26:28, 84, 87, 88, 91, 92, 103:106, 161, 162, 165, 171
A2 (FABA_PSEAE):70, 71, 76:79, 112:116, 15570, 71, 76:79, 112:116, 155

Full PDB list

4b0b, 4b0c, 4b0i, 4b0j, 4b8u, 4cl6, 4fq9

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1 A2
A
2
6
Q
2
7
L
2
8
D
8
4
W
8
7
Q
8
8
G
9
1
F
9
2
G
1
0
3
R
1
0
4
A
1
0
5
L
1
0
6
V
1
6
2
F
1
6
5
F
1
7
1
H
7
0
F
7
1
V
7
6
M
7
7
P
7
8
G
7
9
K
1
1
2
F
1
1
3
F
1
1
4
G
1
1
5
Q
1
1
6
Y
1
5
5
[1]4b0b.a 54f14 . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]4b0c.a c9h11 . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]4b0i.a kbp19 . . . . . . . . . . . . . . - N . . . . . . . . . . .
[1]4b0j.a 3mq12 . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]4b8u.a ibk20 . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]4cl6.c 7sb19 . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]4fq9.a none . . . . . . . . . . . . . . . . . . . . . . . . . . .

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
C
1
5
A
2
6
Q
2
7
L
2
8
D
8
4
W
8
7
Q
8
8
G
9
1
F
9
2
G
1
0
3
R
1
0
4
A
1
0
5
L
1
0
6
R
1
6
1
V
1
6
2
F
1
6
5
F
1
7
1
H
7
0
F
7
1
V
7
6
M
7
7
P
7
8
G
7
9
K
1
1
2
F
1
1
3
F
1
1
4
G
1
1
5
Q
1
1
6
Y
1
5
5
[1]4b0b.a . . . . . . . . . . . . . . . . * . . . . . . . . . . . .
[1]4b0c.a . . . . . . . . . . . . . . . . * . . . . . . . . . . . .
[1]4b0i.a . . . . . . . . . . . . . . . . - N . . . . . . . . . . .
[1]4b0j.a . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]4b8u.a . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]4cl6.c . . . . . . . . . . . . . . . . * . . . . . . . . . . . .
[1]4fq9.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
4b0b.a:54f
4b0c.a:c9h
4b0i.a:kbp
4b0j.a:3mq
4b8u.a:ibk
4cl6.c:7sb
4fq9.a is apo
[1] 4b0b.a
0
0.5 2.3 3.7 3.4 0.4 -
[1] 4b0c.a 0
0
1.8 4.5 3.6 0.1 -
[1] 4b0i.a 0 0
0.2
0.1 0.2 0.5 -
[1] 4b0j.a 0 0 0.3
0
0.1 0.5 -
[1] 4b8u.a 0 0 0 0.3
0
0.1 -
[1] 4cl6.c 0 0 1.1 4.0 3.5
0
-
[1] 4fq9.a 0 0 1.2 4.2 3.4 0.2
-
[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
4b0b.a
4b0c.a
4b0i.a
4b0j.a
4b8u.a
4cl6.c
4fq9.a
[1] 4b0b.a
0
.08 .18 .17 .18 .07 .06
[1] 4b0c.a .08
0
.18 .17 .16 .03 .03
[1] 4b0i.a .18 .18
0
.02 .04 .17 .16
[1] 4b0j.a .17 .17 .02
0
.03 .16 .16
[1] 4b8u.a .18 .16 .04 .03
0
.15 .16
[1] 4cl6.c .07 .03 .17 .16 .15
0
.03
[1] 4fq9.a .06 .03 .16 .16 .16 .03
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
4b0b.a
4b0c.a
4b0i.a
4b0j.a
4b8u.a
4cl6.c
4fq9.a
[1] 4b0b.a
0
0.5 0.3 1.1 0.6 0.4 0.3
[1] 4b0c.a 0.5
0
0.3 1.0 0.7 0.5 0.5
[1] 4b0i.a 0.3 0.3
0
0.2 0.5 0.3 0.2
[1] 4b0j.a 1.1 1.0 0.2
0
1.1 0.9 0.9
[1] 4b8u.a 0.6 0.7 0.5 1.1
0
0.7 0.7
[1] 4cl6.c 0.4 0.5 0.3 0.9 0.7
0
0.3
[1] 4fq9.a 0.3 0.5 0.2 0.9 0.7 0.3
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 0.5 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
4b0b.a
4b0c.a
4b0i.a
4b0j.a
4b8u.a
4cl6.c
4fq9.a
[1] 4b0b.a
0
1.1 1.0 1.5 1.2 0.8 1.0
[1] 4b0c.a 1.1
0
0.5 1.2 0.9 0.8 0.6
[1] 4b0i.a 1.0 0.5
0
0.5 0.8 0.6 0.5
[1] 4b0j.a 1.5 1.2 0.5
0
1.1 1.3 1.2
[1] 4b8u.a 1.2 0.9 0.8 1.1
0
1.0 0.9
[1] 4cl6.c 0.8 0.8 0.6 1.3 1.0
0
0.7
[1] 4fq9.a 1.0 0.6 0.5 1.2 0.9 0.7
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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