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FABH_MYCTU_1_335

3-oxoacyl-[acyl-carrier-protein] synthase 3 [FabH family]

Composition of the binding site

Protein chains homodimer [domain annotation]
A1 (FABH_MYCTU):R: ACP-binding (260, 261, 263)
35, 37:39, 42, 43, 46, 47, 91, 92, 121, 122, 152, 155, 161, 162, 165:167, 199, 201, 205, 216:219, 221, 223, 224, 226, 227, 258, 264, 289, 291, 319:321
35, 37:39, 42, 43, 46, 47, 91, 92, 121, 122, 152, 155, 161, 162, 165:167, 199, 201, 205, 216:219, 221, 223, 224, 226, 227, 258, 260, 261, 263, 264, 289, 291, 319:321
A2 (FABH_MYCTU):96, 97, 20696, 97, 206

Full PDB list

1hzp, 1m1m, 1u6e, 1u6s, 2ahb, 2aj9, 2qnx, 2qny, 2qnz, 2qo0, 2qo1, 2qx1

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1 A2
D
3
7
S
3
8
W
4
2
R
4
6
T
4
7
N
9
1
T
9
2
G
1
2
1
C
1
2
2
L
1
5
2
T
1
5
5
R
1
6
1
I
1
6
6
F
1
6
7
I
1
9
9
Q
2
0
1
W
2
0
5
P
2
1
7
F
2
1
8
V
2
1
9
L
2
2
1
G
2
2
3
P
2
2
4
V
2
2
6
F
2
2
7
H
2
5
8
A
2
6
0
N
2
6
1
I
2
6
4
N
2
8
9
S
2
9
1
Y
3
1
9
G
3
2
0
A
3
2
1
Q
9
6
T
9
7
[1]1hzp.a dao14 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]1m1m.a none . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]1u6e.a none . . . . . . . . A . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]1u6s.a dcc61 . . . . . . . . A . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]2ahb.a none . . . A . . . . . . . A . . . . . . . . . . . . . . . . . . . . . . . .
[1]2aj9.b none . . A . . . . . . . . A . . . . . . . . . . . . . . . . . . . . . . . .
[1]2qnx.a mdx,udt28 . . . . . . . . * . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]2qny.a dfd13 - . . . . . . . * . . . . . . . . . . . . . . . . . F . . . . . . . . .
[1]2qnz.a dfd13 - - . . . . . . * . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]2qo0.b d1t11 . - . . . . . . * . . . . . . . . . . . . . . . . . F . . . . . . . . .
[1]2qo1.a d1t,vzz28 . . . . . . . . * . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]2qx1.a coa,d1t59 . . . . . . . . * . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]2qx1.b d1t11 . . . . . . . . * . . . . . . . . . . . . . . . . . . . . . . . . . . .

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
H
3
5
D
3
7
S
3
8
S
3
9
W
4
2
I
4
3
R
4
6
T
4
7
N
9
1
T
9
2
G
1
2
1
C
1
2
2
L
1
5
2
T
1
5
5
R
1
6
1
G
1
6
2
F
1
6
5
I
1
6
6
F
1
6
7
I
1
9
9
Q
2
0
1
W
2
0
5
R
2
1
6
P
2
1
7
F
2
1
8
V
2
1
9
L
2
2
1
G
2
2
3
P
2
2
4
V
2
2
6
F
2
2
7
H
2
5
8
A
2
6
0
N
2
6
1
R
2
6
3
I
2
6
4
N
2
8
9
S
2
9
1
Y
3
1
9
G
3
2
0
A
3
2
1
Q
9
6
T
9
7
I
2
0
6
[1]1hzp.a . . . . . . . . . . . * . . * . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]1m1m.a . . * . . . . . . . . * . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]1u6e.a . . . . . . . . . . . A . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]1u6s.a . . . . . . . . . . . A . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]2ahb.a . . * . . . A . . . . * . . A . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]2aj9.b . . . . A . . . . . . * . . A . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]2qnx.a . . . . . . . . . . . * . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]2qny.a - - . . * . . . . . . * . . . . . . . . . . . . . . . . . . . . F . . . . . . . . . . .
[1]2qnz.a - - - . . . . . . . . * . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]2qo0.b . . - - . . . . . . . * . . . . . . . . . . . . . . . . . . . . F . . . . . . . . . . .
[1]2qo1.a . . * . . . . . . . . * . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]2qx1.a . . . . . . . . . . . * . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]2qx1.b . . . . . . . . . . . * . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

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
1hzp.a:dao
1m1m.a is apo
1u6e.a is apo
1u6s.a:dcc
2ahb.a is apo
2aj9.b is apo
2qnx.a:mdx,udt
2qny.a:dfd
2qnz.a:dfd
2qo0.b:d1t
2qo1.a:d1t,vzz
2qx1.a:coa,d1t
2qx1.b:d1t
[1] 1hzp.a
0
- - 2.9 - - 1.5 0.7 1.1 0.6 1.0 2.3 0.9
[1] 1m1m.a 0.1
-
- 3.7 - - 1.9 1.4 1.3 1.0 1.3 2.3 1.2
[1] 1u6e.a 0 -
-
0.8 - - 0.3 0 0 0 0.1 0.4 0.1
[1] 1u6s.a 0 - -
0
- - 0.4 0 0.1 0 0.1 0.4 0.1
[1] 2ahb.a 0 - - 2.2
-
- 1.6 0.6 0.8 0.5 0.6 1.7 0.9
[1] 2aj9.b 0.1 - - 1.4 -
-
1.7 1.0 1.1 0.6 0.7 1.1 0.9
[1] 2qnx.a 0 - - 1.3 - -
0.4
0.5 0.3 0.1 0.1 0.3 0.3
[1] 2qny.a 3.4 - - 5.4 - - 3.4
0.4
0.4 0.1 2.5 2.9 0.1
[1] 2qnz.a 0 - - 2.3 - - 0.5 0.6
0.6
0.1 0.3 0.7 0.3
[1] 2qo0.b 3.5 - - 4.4 - - 3.8 0.9 0.6
0.3
2.6 2.1 0.6
[1] 2qo1.a 0.1 - - 1.8 - - 0.9 0.8 0.6 0.3
0.3
1.0 0.4
[1] 2qx1.a 0.1 - - 1.4 - - 1.0 0.8 1.0 0.3 0.7
0.3
0.6
[1] 2qx1.b 0.2 - - 2.0 - - 0.7 0.6 0.7 0.3 0.3 0.8
0.3
[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
1hzp.a
1m1m.a
1u6e.a
1u6s.a
2ahb.a
2aj9.b
2qnx.a
2qny.a
2qnz.a
2qo0.b
2qo1.a
2qx1.a
2qx1.b
[1] 1hzp.a
0
.06 .08 .09 .07 .07 .06 .16 .06 .16 .07 .07 .06
[1] 1m1m.a .06
0
.09 .10 .04 .06 .07 .17 .08 .17 .05 .07 .07
[1] 1u6e.a .08 .09
0
.02 .05 .06 .03 .15 .06 .13 .04 .04 .05
[1] 1u6s.a .09 .10 .02
0
.06 .07 .04 .15 .06 .13 .05 .04 .06
[1] 2ahb.a .07 .04 .05 .06
0
.04 .05 .16 .08 .13 .02 .04 .06
[1] 2aj9.b .07 .06 .06 .07 .04
0
.07 .17 .08 .13 .04 .05 .08
[1] 2qnx.a .06 .07 .03 .04 .05 .07
0
.13 .04 .13 .03 .02 .03
[1] 2qny.a .16 .17 .15 .15 .16 .17 .13
0
.10 .08 .15 .13 .10
[1] 2qnz.a .06 .08 .06 .06 .08 .08 .04 .10
0
.15 .06 .05 .02
[1] 2qo0.b .16 .17 .13 .13 .13 .13 .13 .08 .15
0
.12 .11 .13
[1] 2qo1.a .07 .05 .04 .05 .02 .04 .03 .15 .06 .12
0
.02 .05
[1] 2qx1.a .07 .07 .04 .04 .04 .05 .02 .13 .05 .11 .02
0
.04
[1] 2qx1.b .06 .07 .05 .06 .06 .08 .03 .10 .02 .13 .05 .04
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 1.0 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
1hzp.a
1m1m.a
1u6e.a
1u6s.a
2ahb.a
2aj9.b
2qnx.a
2qny.a
2qnz.a
2qo0.b
2qo1.a
2qx1.a
2qx1.b
[1] 1hzp.a
0
0.5 0.2 0.3 0.3 0.3 0.5 1.1 0.4 1.4 0.3 0.3 0.4
[1] 1m1m.a 0.5
0
0.6 0.6 0.4 0.5 0.7 1.4 0.7 1.4 0.6 0.6 0.6
[1] 1u6e.a 0.2 0.6
0
0.3 0.4 0.3 0.5 1.0 0.4 1.4 0.3 0.4 0.4
[1] 1u6s.a 0.3 0.6 0.3
0
0.4 0.4 0.5 1.1 0.3 1.5 0.3 0.4 0.5
[1] 2ahb.a 0.3 0.4 0.4 0.4
0
0.4 0.5 1.1 0.4 1.4 0.3 0.4 0.5
[1] 2aj9.b 0.3 0.5 0.3 0.4 0.4
0
0.6 1.2 0.4 1.5 0.4 0.4 0.5
[1] 2qnx.a 0.5 0.7 0.5 0.5 0.5 0.6
0
0.9 0.3 1.4 0.4 0.4 0.5
[1] 2qny.a 1.1 1.4 1.0 1.1 1.1 1.2 0.9
0
0.3 0.4 1.0 1.0 1.0
[1] 2qnz.a 0.4 0.7 0.4 0.3 0.4 0.4 0.3 0.3
0
0.4 0.3 0.3 0.3
[1] 2qo0.b 1.4 1.4 1.4 1.5 1.4 1.5 1.4 0.4 0.4
0
1.4 1.5 1.5
[1] 2qo1.a 0.3 0.6 0.3 0.3 0.3 0.4 0.4 1.0 0.3 1.4
0
0.3 0.4
[1] 2qx1.a 0.3 0.6 0.4 0.4 0.4 0.4 0.4 1.0 0.3 1.5 0.3
0
0.4
[1] 2qx1.b 0.4 0.6 0.4 0.5 0.5 0.5 0.5 1.0 0.3 1.5 0.4 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

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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
1hzp.a
1m1m.a
1u6e.a
1u6s.a
2ahb.a
2aj9.b
2qnx.a
2qny.a
2qnz.a
2qo0.b
2qo1.a
2qx1.a
2qx1.b
[1] 1hzp.a
0
1.2 0.6 0.9 1.0 1.0 1.0 1.3 0.9 2.2 0.9 1.0 1.0
[1] 1m1m.a 1.2
0
1.2 1.5 0.7 0.9 1.5 1.9 1.6 2.5 1.5 1.5 1.5
[1] 1u6e.a 0.6 1.2
0
0.9 1.0 1.0 1.0 1.3 0.9 2.3 0.9 1.0 1.0
[1] 1u6s.a 0.9 1.5 0.9
0
1.3 1.2 0.6 1.1 0.6 2.2 0.6 0.6 0.8
[1] 2ahb.a 1.0 0.7 1.0 1.3
0
0.7 1.3 1.6 1.3 2.5 1.2 1.3 1.3
[1] 2aj9.b 1.0 0.9 1.0 1.2 0.7
0
1.2 1.6 1.2 2.2 1.2 1.2 1.2
[1] 2qnx.a 1.0 1.5 1.0 0.6 1.3 1.2
0
0.9 0.5 1.7 0.7 0.7 0.7
[1] 2qny.a 1.3 1.9 1.3 1.1 1.6 1.6 0.9
0
0.5 1.3 1.0 1.1 1.0
[1] 2qnz.a 0.9 1.6 0.9 0.6 1.3 1.2 0.5 0.5
0
1.2 0.4 0.5 0.5
[1] 2qo0.b 2.2 2.5 2.3 2.2 2.5 2.2 1.7 1.3 1.2
0
1.6 2.2 2.2
[1] 2qo1.a 0.9 1.5 0.9 0.6 1.2 1.2 0.7 1.0 0.4 1.6
0
0.6 0.6
[1] 2qx1.a 1.0 1.5 1.0 0.6 1.3 1.2 0.7 1.1 0.5 2.2 0.6
0
0.7
[1] 2qx1.b 1.0 1.5 1.0 0.8 1.3 1.2 0.7 1.0 0.5 2.2 0.6 0.7
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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