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FAB1_MYCTU_1_416

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

Composition of the binding site

Protein chains monomer
A1 (FAB1_MYCTU):171, 210, 215, 237, 239, 273, 276:280, 311, 313, 315, 318, 345, 347, 402:406, 408171, 210, 215, 237, 239, 273, 276:280, 311, 313, 315, 318, 345, 347, 402:406, 408
Cofactors (cF):6u5/m7u
Metals (Me):Na/K

Full PDB list

2wgd, 2wge, 2wgf, 2wgg, 4c6u, 4c6v, 4c6w, 4c6x, 4c6z, 4c70, 4c71, 4c72, 4c73, 5ld8 (redundant Pocketome entry)

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1 cF Me
C
1
7
1
F
2
1
0
A
2
1
5
F
2
3
7
F
2
3
9
D
2
7
3
H
2
7
6
M
2
7
7
V
2
7
8
A
2
7
9
P
2
8
0
H
3
1
1
T
3
1
3
T
3
1
5
G
3
1
8
H
3
4
5
I
3
4
7
F
4
0
2
G
4
0
3
F
4
0
4
G
4
0
5
G
4
0
6
N
4
0
8
[1]2wge.a tlm14 . . . . . . . . . . . . . . . . . . . . . . . Na
[1]2wgf.d none Q . . . . . . . . . . . . . . . . . . . . . . Na
[1]4c6u.a tlg16 . . . . . . . . . . . . . . . . . . . . . . . K
[1]4c6x.b tlm14 Q . . . . . . . . . . . . . . . . . . . . . . m7u K
[1]4c6z.a tle15 Q . . . . . . . . . . . . . . . . . . . . . . m7u K
[1]4c70.a tlj16 Q . . . . . . . . . . . . . . . . . . . . . . m7u K
[1]4c71.b 7rd20 Q . . . . . . . . . . . . . . . . . . . . . . m7u K
[1]4c72.b tlg16 Q . . . . . . . . . . . . . . . . . . . . . . m7u K
[1]4c73.b tlh19 Q . . . . . . . . . . . . . . . . . . . . . . m7u K
[1]5ld8.b none . . . . . . . . . . . . . . . . . . . . . . . 6u5 Na

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 cF Me
C
1
7
1
F
2
1
0
A
2
1
5
F
2
3
7
F
2
3
9
D
2
7
3
H
2
7
6
M
2
7
7
V
2
7
8
A
2
7
9
P
2
8
0
H
3
1
1
T
3
1
3
T
3
1
5
G
3
1
8
H
3
4
5
I
3
4
7
F
4
0
2
G
4
0
3
F
4
0
4
G
4
0
5
G
4
0
6
N
4
0
8
[1]2wge.a . . . . . . . . . . . . . . . . . . . . . . . Na
[1]2wgf.d Q . . . . . . . . . . . . . . . . . . . . . . Na
[1]4c6u.a . . . . . . . . . . . . . . . . . . . . . . . K
[1]4c6x.b Q . . . . . . . . . . . . . . . . . . . . . . m7u K
[1]4c6z.a Q . . . . . . . . . . . . . . . * . . . . . . m7u K
[1]4c70.a Q . . . . . . . . . . . . . . . * . . . . . . m7u K
[1]4c71.b Q . . . . . . . . . . . . . . . . . . . . . . m7u K
[1]4c72.b Q . . . . . . . . . . . . . . . . . . . . . . m7u K
[1]4c73.b Q . . . . . . . . . . . . . . . . . . . . . . m7u K
[1]5ld8.b . . . . . . . . . . . . . . . . . . . * . . . 6u5 Na

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
2wge.a:tlm
2wgf.d is apo
4c6u.a:tlg
4c6x.b:tlm
4c6z.a:tle
4c70.a:tlj
4c71.b:7rd
4c72.b:tlg
4c73.b:tlh
5ld8.b is apo
[1] 2wge.a
0.3
- 0.1 0.7 0.9 0.9 1.8 0.6 1.1 -
[1] 2wgf.d 0.5
-
0.2 0.5 0.5 0.5 1.2 0.5 0.7 -
[1] 4c6u.a 0.1 -
0.1
0.7 0.7 0.9 1.1 0.7 0.6 -
[1] 4c6x.b 0 - 0
0
0 0.2 0.6 0 0.2 -
[1] 4c6z.a 0 - 0 0
0
0 0.5 0 0.2 -
[1] 4c70.a 0 - 0 0 0
0
0.5 0 0.2 -
[1] 4c71.b 0 - 0 0 0 0
0.3
0 0.1 -
[1] 4c72.b 0 - 0 0 0 0 0.3
0
0.2 -
[1] 4c73.b 0 - 0 0 0 0 0.3 0
0
-
[1] 5ld8.b 0.4 - 0.8 1.0 1.0 1.2 1.6 0.6 1.0
-
[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
2wge.a
2wgf.d
4c6u.a
4c6x.b
4c6z.a
4c70.a
4c71.b
4c72.b
4c73.b
5ld8.b
[1] 2wge.a
0
.06 .04 .07 .07 .07 .07 .07 .07 .06
[1] 2wgf.d .06
0
.06 .05 .05 .05 .04 .04 .05 .07
[1] 4c6u.a .04 .06
0
.06 .07 .07 .07 .07 .07 .06
[1] 4c6x.b .07 .05 .06
0
.02 .02 .01 .01 .02 .06
[1] 4c6z.a .07 .05 .07 .02
0
0 .01 .01 .02 .08
[1] 4c70.a .07 .05 .07 .02 0
0
.01 .01 .02 .08
[1] 4c71.b .07 .04 .07 .01 .01 .01
0
0 0 .07
[1] 4c72.b .07 .04 .07 .01 .01 .01 0
0
.01 .07
[1] 4c73.b .07 .05 .07 .02 .02 .02 0 .01
0
.08
[1] 5ld8.b .06 .07 .06 .06 .08 .08 .07 .07 .08
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
2wge.a
2wgf.d
4c6u.a
4c6x.b
4c6z.a
4c70.a
4c71.b
4c72.b
4c73.b
5ld8.b
[1] 2wge.a
0
0.5 0.2 0.6 0.6 0.5 0.6 0.6 0.6 0.6
[1] 2wgf.d 0.5
0
0.5 0.4 0.5 0.4 0.5 0.4 0.4 0.4
[1] 4c6u.a 0.2 0.5
0
0.5 0.6 0.5 0.6 0.5 0.5 0.5
[1] 4c6x.b 0.6 0.4 0.5
0
0.2 0.1 0.2 0.1 0.1 0.4
[1] 4c6z.a 0.6 0.5 0.6 0.2
0
0.2 0.1 0.2 0.2 0.5
[1] 4c70.a 0.5 0.4 0.5 0.1 0.2
0
0.2 0.1 0.1 0.5
[1] 4c71.b 0.6 0.5 0.6 0.2 0.1 0.2
0
0.2 0.2 0.5
[1] 4c72.b 0.6 0.4 0.5 0.1 0.2 0.1 0.2
0
0.1 0.4
[1] 4c73.b 0.6 0.4 0.5 0.1 0.2 0.1 0.2 0.1
0
0.5
[1] 5ld8.b 0.6 0.4 0.5 0.4 0.5 0.5 0.5 0.4 0.5
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
2wge.a
2wgf.d
4c6u.a
4c6x.b
4c6z.a
4c70.a
4c71.b
4c72.b
4c73.b
5ld8.b
[1] 2wge.a
0
0.7 0.3 0.8 0.8 0.7 0.9 0.8 0.7 0.6
[1] 2wgf.d 0.7
0
0.6 0.5 0.5 0.4 0.6 0.5 0.4 0.5
[1] 4c6u.a 0.3 0.6
0
0.7 0.7 0.6 0.8 0.7 0.6 0.6
[1] 4c6x.b 0.8 0.5 0.7
0
0.3 0.3 0.5 0.2 0.3 0.6
[1] 4c6z.a 0.8 0.5 0.7 0.3
0
0.3 0.4 0.2 0.4 0.7
[1] 4c70.a 0.7 0.4 0.6 0.3 0.3
0
0.5 0.3 0.2 0.6
[1] 4c71.b 0.9 0.6 0.8 0.5 0.4 0.5
0
0.5 0.5 0.8
[1] 4c72.b 0.8 0.5 0.7 0.2 0.2 0.3 0.5
0
0.3 0.6
[1] 4c73.b 0.7 0.4 0.6 0.3 0.4 0.2 0.5 0.3
0
0.6
[1] 5ld8.b 0.6 0.5 0.6 0.6 0.7 0.6 0.8 0.6 0.6
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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