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FABA_YERPE_1_172

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

Composition of the binding site

Protein chains homodimer
A1 (FABA_YERPE):71, 78:80, 114:117, 15671, 78:80, 114:117, 156
A2 (FABA_YERPE):105:107, 166, 170, 172105:107, 166, 170, 172

Full PDB list

3q62, 5f6r, 5hd6

Pocket contact map

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PDB.ch
   
ligand
A1 A2
H
7
1
P
7
9
G
8
0
F
1
1
4
T
1
1
5
G
1
1
6
Q
1
1
7
R
1
0
5
A
1
0
6
L
1
0
7
[1]3q62.b none . . . . . . . . . .
[1]5f6r.a 5vo15 . . . . . . . . . .
[2]5hd6.a none . . . . . . . . . .
[3]5hd6.b 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

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PDB.ch
A1 A2
H
7
1
M
7
8
P
7
9
G
8
0
F
1
1
4
T
1
1
5
G
1
1
6
Q
1
1
7
Y
1
5
6
R
1
0
5
A
1
0
6
L
1
0
7
F
1
6
6
N
1
7
0
F
1
7
2
[1]3q62.b . . . . . . . . . . . . . - -
[1]5f6r.a . . . . . . . . . . . . . - -
[2]5hd6.a . * . . . . . . . . . . . - *
[3]5hd6.b . * . . . . . . . . . . . F -

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
3q62.b is apo
5f6r.a:5vo
5hd6.a is apo
5hd6.b is apo
[1] 3q62.b
-
0 - -
[1] 5f6r.a -
0
- -
[2] 5hd6.a - 4.6
-
-
[3] 5hd6.b - 4.6 -
-
[Pocket-ligand steric clashes matrix]

Pocket clash dissimilarity (3 clusters)

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
3q62.b
5f6r.a
5hd6.a
5hd6.b
[1] 3q62.b
0
0 .31 .31
[1] 5f6r.a 0
0
.31 .31
[2] 5hd6.a .31 .31
0
.61
[3] 5hd6.b .31 .31 .61
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
3q62.b
5f6r.a
5hd6.a
5hd6.b
[1] 3q62.b
0
0.3 0.5 0.5
[1] 5f6r.a 0.3
0
0.3 0.3
[2] 5hd6.a 0.5 0.3
0
0
[3] 5hd6.b 0.5 0.3 0
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
3q62.b
5f6r.a
5hd6.a
5hd6.b
[1] 3q62.b
0
0.3 0.7 0.7
[1] 5f6r.a 0.3
0
0.6 0.6
[2] 5hd6.a 0.7 0.6
0
0
[3] 5hd6.b 0.7 0.6 0
0
[Binding site full-atom RMSD matrix]







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[ENTRY 2D visualization]

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