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FABG_PSEAE_1_247

3-oxoacyl-[acyl-carrier-protein] reductase FabG [Short-chain dehydrogenases/reductases (SDR) family]

Composition of the binding site

Protein chains homodimer
A1 (FABG_PSEAE):106, 107, 110, 111, 114, 115, 156, 157, 159, 160, 163, 164, 167106, 107, 110, 111, 114, 115, 156, 157, 159, 160, 163, 164, 167
A2 (FABG_PSEAE):106, 107, 110, 111, 114, 115, 156, 159, 160, 163, 164, 167106, 107, 110, 111, 114, 115, 156, 159, 160, 163, 164, 167

Full PDB list

4afn, 4ag3, 4bnt, 4bnu, 4bnv, 4bnw, 4bnx, 4bny, 4bnz, 4bo0, 4bo1, 4bo2, 4bo3, 4bo4, 4bo5, 4bo6, 4bo7, 4bo8, 4bo9 (redundant Pocketome entry)

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1 A2
W
1
0
6
F
1
0
7
V
1
1
0
N
1
1
1
L
1
1
4
A
1
5
6
A
1
5
9
G
1
6
0
G
1
6
3
F
1
6
4
W
1
0
6
F
1
0
7
V
1
1
0
N
1
1
1
L
1
1
4
A
1
5
6
A
1
5
9
G
1
6
0
G
1
6
3
F
1
6
4
A
1
6
7
[1]4bnt.c 36e13 . . . . . . . . . . . . . . . . . . . . .
[1]4bnu.a 9kq21 . . . . . . . . . . . . . . . . . . . . .
[1]4bnv.a q7u21 . . . . . . . . . . . . . . . . . . . . .
[1]4bnw.c none . . . . . . . . . . . . . . . . . . . . .
[1]4bnx.a o7425 . . . . . . . . . . . . . . . . . . . . .
[1]4bny.b 36i21 . . . . . . . . . . . . . . . . . . . . .
[1]4bnz.a 8m519 . . . . . . . . . . . . . . . . . . . . .
[1]4bo0.c fxe24 . . . . . . . . . . . . . . . . . . . . .
[1]4bo1.c nkh24 . . . . . . . . . . . . . . . . . . . . .
[1]4bo2.d 36k23 . . . . . . . . . . . . . . . . . . . . .
[1]4bo3.a u9821 . . . . . . . . . . . . . . . . . . . . .
[1]4bo4.b 36g21 . . . . . . . . . . . . . . . . . . . . .
[1]4bo5.a wi419 . . . . . . . . . . . . . . . . . . . . .
[1]4bo6.b 36p21 . . . . . . . . . . . . . . . . . . . . .
[1]4bo7.a j2t19 . . . . . . . . . . . . . . . . . . . . .
[1]4bo8.a 34x23 . . . . . . . . . . . . . . . . . . . . .
[1]4bo9.a 3x324 . . . . . . . . . . . . . . . . . . . . .

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
W
1
0
6
F
1
0
7
V
1
1
0
N
1
1
1
L
1
1
4
N
1
1
5
A
1
5
6
A
1
5
7
A
1
5
9
G
1
6
0
G
1
6
3
F
1
6
4
A
1
6
7
W
1
0
6
F
1
0
7
V
1
1
0
N
1
1
1
L
1
1
4
N
1
1
5
A
1
5
6
A
1
5
9
G
1
6
0
G
1
6
3
F
1
6
4
A
1
6
7
[1]4bnt.c . . . * . . . . . . . . . . . . . . . . . . . . .
[1]4bnu.a . . . . . . . . . . . . . . . . . . . . . . . . .
[1]4bnv.a . . . . . . . . . . . . . . . . . . . . . . . . .
[1]4bnw.c . . . . . . . . . . . . . . . . . . . . . . . . .
[1]4bnx.a . . . . . . . . . . . . . . . . . . . . . . . . .
[1]4bny.b . . . . . . . . . . . . . . . . . . . . . . . . .
[1]4bnz.a . . . . . . . . . . . . . . . . . . . . . . . . .
[1]4bo0.c . . . . . . . . . . . . . . . . . . . . . . . . .
[1]4bo1.c . . . . . . . . . . . . . . . . . . . . . . . . .
[1]4bo2.d . . . . . . . . . . . . . . . . * . . . . . . . .
[1]4bo3.a . . . * . . . . . . . . . . . . . . . . . . . . .
[1]4bo4.b . . . . . . . . . . . . . . . . * . . . . . . . .
[1]4bo5.a . . . . . . . . . . . . . . . . . . . . . . . . .
[1]4bo6.b . . . . . . . . . . . . . . . . * . . . . . . . .
[1]4bo7.a . . . * . . . . . . . . . . . . * . . . . . . . .
[1]4bo8.a . . . . . . . . . . . . . . . . . . . . . . . . .
[1]4bo9.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
4bnt.c:36e
4bnu.a:9kq
4bnv.a:q7u
4bnw.c is apo
4bnx.a:o74
4bny.b:36i
4bnz.a:8m5
4bo0.c:fxe
4bo1.c:nkh
4bo2.d:36k
4bo3.a:u98
4bo4.b:36g
4bo5.a:wi4
4bo6.b:36p
4bo7.a:j2t
4bo8.a:34x
4bo9.a:3x3
[1] 4bnt.c
0
0 0.2 - 1.3 0.6 0.2 0.5 1.6 0.7 0.6 0.1 0.2 0.5 0 0.8 1.2
[1] 4bnu.a 0.1
0
0.2 - 0.2 0.2 0.1 0.3 0.6 0.3 0.3 0.1 0 0.4 0 0.2 0.2
[1] 4bnv.a 0 0.2
0.1
- 1.0 0.3 0 0 0.3 0.2 0.1 0.1 0.3 0.1 0 0.3 0.6
[1] 4bnw.c 0 0.3 0.3
-
1.1 0.7 0 0.3 0.8 0.5 0.6 0.1 0.6 0.2 0 0.2 0.6
[1] 4bnx.a 0.2 0 0.2 -
0.1
0 0 0.3 0.5 0 0.2 0 0 0.2 0 0 0
[1] 4bny.b 0.1 0 0.1 - 0.2
0
0.1 0.3 0.8 0.3 0.3 0 0 0.4 0 0 0
[1] 4bnz.a 0 0.1 0 - 0.8 0.3
0
0.1 0.2 0.1 0.1 0.1 0.1 0 0 0.2 0.4
[1] 4bo0.c 0 0 0.1 - 0.7 0.3 0
0
0.3 0.1 0 0.1 0.1 0.2 0 0.1 0.4
[1] 4bo1.c 0 0 0.1 - 0.2 0.2 0 0.1
0
0.2 0.1 0.1 0.1 0.2 0 0 0.1
[1] 4bo2.d 0.2 0.7 0 - 1.0 0.2 0 0.3 0.6
0.1
0.1 0 0.1 0.2 0 0.5 0.6
[1] 4bo3.a 1.0 0.1 1.4 - 1.4 1.4 1.0 0.9 1.3 1.3
0
1.2 0.3 1.1 0.7 0.8 1.2
[1] 4bo4.b 0 0.5 0.1 - 1.1 0.2 0 0.3 0.6 0.1 0.1
0
0.1 0.2 0 0.2 0.7
[1] 4bo5.a 0.2 0.2 0.1 - 0.8 0.3 0 0.3 0.2 0.2 0.2 0.1
0
0.2 0.1 0.2 0.4
[1] 4bo6.b 0 0.5 0.1 - 1.2 0.2 0 0.1 0.2 0.3 0.1 0.1 0.1
0
0 0.2 0.8
[1] 4bo7.a 0 0.4 0.1 - 1.2 0.3 0 0.4 0.5 0.2 0.1 0.1 0.2 0.2
0
0.4 1.0
[1] 4bo8.a 0.1 0.1 0 - 0.7 0.3 0 0.2 0.4 0.2 0.1 0.1 0.2 0.2 0
0.2
0.3
[1] 4bo9.a 0 0 0 - 0.2 0 0 0.1 0.4 0.3 0.1 0 0 0.1 0 0
0
[Pocket-ligand steric clashes matrix]

Pocket clash dissimilarity (1 cluster)

Pockets (x) vs pockets (y) colored by ligand clash profile difference

zoom: [−] [+]; [view as image]; [download as text]

pocketpocket
≥1.
.9
.8
.7
.6
.5
.4
.3
.2
.1
.0
4bnt.c
4bnu.a
4bnv.a
4bnw.c
4bnx.a
4bny.b
4bnz.a
4bo0.c
4bo1.c
4bo2.d
4bo3.a
4bo4.b
4bo5.a
4bo6.b
4bo7.a
4bo8.a
4bo9.a
[1] 4bnt.c
0
.07 .10 .13 .10 .07 .10 .09 .10 .09 .08 .08 .10 .10 .09 .09 .09
[1] 4bnu.a .07
0
.07 .11 .04 .02 .06 .05 .03 .07 .10 .07 .05 .08 .07 .05 .05
[1] 4bnv.a .10 .07
0
.07 .08 .09 .02 .03 .05 .05 .08 .04 .03 .04 .03 .02 .06
[1] 4bnw.c .13 .11 .07
0
.12 .12 .09 .07 .08 .11 .14 .10 .08 .10 .10 .08 .10
[1] 4bnx.a .10 .04 .08 .12
0
.04 .07 .05 .05 .07 .10 .06 .06 .10 .08 .06 .03
[1] 4bny.b .07 .02 .09 .12 .04
0
.08 .07 .05 .07 .10 .08 .07 .10 .09 .07 .03
[1] 4bnz.a .10 .06 .02 .09 .07 .08
0
.03 .04 .05 .08 .05 .02 .04 .04 .03 .05
[1] 4bo0.c .09 .05 .03 .07 .05 .07 .03
0
.04 .06 .08 .05 .02 .06 .04 .03 .05
[1] 4bo1.c .10 .03 .05 .08 .05 .05 .04 .04
0
.07 .09 .06 .04 .05 .05 .05 .03
[1] 4bo2.d .09 .07 .05 .11 .07 .07 .05 .06 .07
0
.10 .03 .04 .05 .04 .05 .07
[1] 4bo3.a .08 .10 .08 .14 .10 .10 .08 .08 .09 .10
0
.08 .08 .08 .07 .09 .10
[1] 4bo4.b .08 .07 .04 .10 .06 .08 .05 .05 .06 .03 .08
0
.05 .03 .03 .04 .07
[1] 4bo5.a .10 .05 .03 .08 .06 .07 .02 .02 .04 .04 .08 .05
0
.05 .03 .02 .05
[1] 4bo6.b .10 .08 .04 .10 .10 .10 .04 .06 .05 .05 .08 .03 .05
0
.03 .06 .07
[1] 4bo7.a .09 .07 .03 .10 .08 .09 .04 .04 .05 .04 .07 .03 .03 .03
0
.04 .07
[1] 4bo8.a .09 .05 .02 .08 .06 .07 .03 .03 .05 .05 .09 .04 .02 .06 .04
0
.06
[1] 4bo9.a .09 .05 .06 .10 .03 .03 .05 .05 .03 .07 .10 .07 .05 .07 .07 .06
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

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
4bnt.c
4bnu.a
4bnv.a
4bnw.c
4bnx.a
4bny.b
4bnz.a
4bo0.c
4bo1.c
4bo2.d
4bo3.a
4bo4.b
4bo5.a
4bo6.b
4bo7.a
4bo8.a
4bo9.a
[1] 4bnt.c
0
0.5 0.5 1.0 0.6 0.5 0.4 0.3 0.3 0.3 0.7 0.3 0.3 0.4 0.5 0.3 0.5
[1] 4bnu.a 0.5
0
0.3 0.9 0.2 0.2 0.3 0.4 0.3 0.4 0.4 0.4 0.3 0.5 0.3 0.3 0.3
[1] 4bnv.a 0.5 0.3
0
0.8 0.5 0.3 0.3 0.4 0.3 0.5 0.5 0.4 0.4 0.4 0.3 0.3 0.4
[1] 4bnw.c 1.0 0.9 0.8
0
1.1 0.9 0.9 0.9 0.9 1.0 1.0 1.0 1.0 0.9 1.0 0.9 1.0
[1] 4bnx.a 0.6 0.2 0.5 1.1
0
0.3 0.4 0.5 0.4 0.5 0.4 0.4 0.3 0.6 0.3 0.4 0.3
[1] 4bny.b 0.5 0.2 0.3 0.9 0.3
0
0.3 0.4 0.3 0.4 0.4 0.3 0.3 0.5 0.3 0.3 0.3
[1] 4bnz.a 0.4 0.3 0.3 0.9 0.4 0.3
0
0.4 0.3 0.3 0.5 0.3 0.3 0.4 0.4 0.2 0.4
[1] 4bo0.c 0.3 0.4 0.4 0.9 0.5 0.4 0.4
0
0.3 0.3 0.6 0.3 0.3 0.4 0.5 0.3 0.5
[1] 4bo1.c 0.3 0.3 0.3 0.9 0.4 0.3 0.3 0.3
0
0.4 0.6 0.3 0.3 0.3 0.4 0.3 0.3
[1] 4bo2.d 0.3 0.4 0.5 1.0 0.5 0.4 0.3 0.3 0.4
0
0.6 0.2 0.3 0.5 0.5 0.3 0.5
[1] 4bo3.a 0.7 0.4 0.5 1.0 0.4 0.4 0.5 0.6 0.6 0.6
0
0.5 0.5 0.6 0.4 0.5 0.5
[1] 4bo4.b 0.3 0.4 0.4 1.0 0.4 0.3 0.3 0.3 0.3 0.2 0.5
0
0.3 0.4 0.4 0.3 0.4
[1] 4bo5.a 0.3 0.3 0.4 1.0 0.3 0.3 0.3 0.3 0.3 0.3 0.5 0.3
0
0.4 0.4 0.3 0.3
[1] 4bo6.b 0.4 0.5 0.4 0.9 0.6 0.5 0.4 0.4 0.3 0.5 0.6 0.4 0.4
0
0.5 0.4 0.5
[1] 4bo7.a 0.5 0.3 0.3 1.0 0.3 0.3 0.4 0.5 0.4 0.5 0.4 0.4 0.4 0.5
0
0.4 0.5
[1] 4bo8.a 0.3 0.3 0.3 0.9 0.4 0.3 0.2 0.3 0.3 0.3 0.5 0.3 0.3 0.4 0.4
0
0.4
[1] 4bo9.a 0.5 0.3 0.4 1.0 0.3 0.3 0.4 0.5 0.3 0.5 0.5 0.4 0.3 0.5 0.5 0.4
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

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
4bnt.c
4bnu.a
4bnv.a
4bnw.c
4bnx.a
4bny.b
4bnz.a
4bo0.c
4bo1.c
4bo2.d
4bo3.a
4bo4.b
4bo5.a
4bo6.b
4bo7.a
4bo8.a
4bo9.a
[1] 4bnt.c
0
0.6 0.8 1.1 0.7 0.6 0.7 0.8 0.7 0.6 1.0 0.7 0.6 1.0 0.8 0.6 0.8
[1] 4bnu.a 0.6
0
0.6 1.1 0.3 0.4 0.6 0.9 0.7 0.6 0.8 0.7 0.6 1.1 0.6 0.5 0.7
[1] 4bnv.a 0.8 0.6
0
1.1 0.7 0.7 0.5 0.7 0.6 0.8 0.8 0.6 0.5 0.7 0.4 0.7 0.5
[1] 4bnw.c 1.1 1.1 1.1
0
1.2 1.0 1.1 1.1 0.9 1.1 1.2 1.2 1.2 1.2 1.3 1.0 1.2
[1] 4bnx.a 0.7 0.3 0.7 1.2
0
0.5 0.6 0.9 0.7 0.7 0.8 0.8 0.6 1.1 0.7 0.6 0.7
[1] 4bny.b 0.6 0.4 0.7 1.0 0.5
0
0.7 0.8 0.6 0.5 0.9 0.6 0.7 1.0 0.7 0.4 0.7
[1] 4bnz.a 0.7 0.6 0.5 1.1 0.6 0.7
0
0.8 0.7 0.7 0.9 0.7 0.5 0.9 0.6 0.5 0.6
[1] 4bo0.c 0.8 0.9 0.7 1.1 0.9 0.8 0.8
0
0.6 0.8 1.0 0.6 0.6 0.8 0.7 0.8 0.6
[1] 4bo1.c 0.7 0.7 0.6 0.9 0.7 0.6 0.7 0.6
0
0.7 0.8 0.6 0.6 0.8 0.7 0.6 0.6
[1] 4bo2.d 0.6 0.6 0.8 1.1 0.7 0.5 0.7 0.8 0.7
0
0.9 0.6 0.7 1.0 0.8 0.5 0.8
[1] 4bo3.a 1.0 0.8 0.8 1.2 0.8 0.9 0.9 1.0 0.8 0.9
0
0.8 0.8 1.1 0.8 0.9 0.8
[1] 4bo4.b 0.7 0.7 0.6 1.2 0.8 0.6 0.7 0.6 0.6 0.6 0.8
0
0.4 0.8 0.5 0.6 0.5
[1] 4bo5.a 0.6 0.6 0.5 1.2 0.6 0.7 0.5 0.6 0.6 0.7 0.8 0.4
0
0.9 0.4 0.7 0.4
[1] 4bo6.b 1.0 1.1 0.7 1.2 1.1 1.0 0.9 0.8 0.8 1.0 1.1 0.8 0.9
0
0.9 0.9 0.8
[1] 4bo7.a 0.8 0.6 0.4 1.3 0.7 0.7 0.6 0.7 0.7 0.8 0.8 0.5 0.4 0.9
0
0.8 0.6
[1] 4bo8.a 0.6 0.5 0.7 1.0 0.6 0.4 0.5 0.8 0.6 0.5 0.9 0.6 0.7 0.9 0.8
0
0.7
[1] 4bo9.a 0.8 0.7 0.5 1.2 0.7 0.7 0.6 0.6 0.6 0.8 0.8 0.5 0.4 0.8 0.6 0.7
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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