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FABH_ECOLI_1_317

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

Composition of the binding site

Protein chains monomer [domain annotation]
A1 (FABH_ECOLI):R: ACP-binding (246, 247, 249)
27, 28, 32, 36, 37, 112, 151, 152, 155:157, 189, 207, 209, 210, 212, 213, 216, 244, 250, 274, 304, 305
27, 28, 32, 36, 37, 112, 151, 152, 155:157, 189, 207, 209, 210, 212, 213, 216, 244, 246, 247, 249, 250, 274, 304, 305

Full PDB list

1ebl, 1hn9, 1hnd, 1hnh, 1hnj, 1hnk, 1mzs, 2eft, 2gyo, 3il9, 4z8d, 5bnm, 5bnr, 5bns (redundant Pocketome entry)

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1
T
2
8
W
3
2
R
3
6
T
3
7
C
1
1
2
R
1
5
1
G
1
5
2
I
1
5
5
I
1
5
6
F
1
5
7
L
1
8
9
M
2
0
7
G
2
0
9
N
2
1
0
V
2
1
2
F
2
1
3
A
2
1
6
H
2
4
4
A
2
4
6
N
2
4
7
R
2
4
9
I
2
5
0
N
2
7
4
F
3
0
4
[1]1hn9.a none . . . . . . . . . . . . . . . . . . . . . . . .
[1]1hnd.a coa48 . . . . . . . . . . . . . . . . . . . . . . . .
[1]1hnh.a coa48 . . . . * . . . . . . * . . . . . . . . . . . .
[1]1hnj.a mlc41 . . . . . . . . . . . . . . . . . . . . . . . .
[1]1mzs.a 66930 . . . . * . . . . . . . . . . . . . . . . . . .
[1]2eft.a coa48 . . . . . . . . . . . . . . . . . . . . . . . .
[1]4z8d.a 4lb22 . . . . . . . . . . . . . . . . . . . . . . . .
[1]5bnm.a 4vk25 . . . . . . . . . . . . . . . . . . . . . . . .
[1]5bnr.a 4vl24 . . . . . . . . . . . . . . . . . . . . . . . .
[1]5bns.a 4vm35 . . . . . . . . . . . . . . . . . . . . . . . .
[2]1ebl.a coa48 . . . . . . . . . . . * . . . . . . . . . . . .
[2]3il9.a none . . . . * . . . . . . . . . . . . . . . . . . .
[3]5bnm.b pg413 . . . . . . . . . . . . . . . . . . . . . . . .

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
D
2
7
T
2
8
W
3
2
R
3
6
T
3
7
C
1
1
2
R
1
5
1
G
1
5
2
I
1
5
5
I
1
5
6
F
1
5
7
L
1
8
9
M
2
0
7
G
2
0
9
N
2
1
0
V
2
1
2
F
2
1
3
A
2
1
6
H
2
4
4
A
2
4
6
N
2
4
7
R
2
4
9
I
2
5
0
N
2
7
4
F
3
0
4
G
3
0
5
[1]1hn9.a . . . . . . * . . . . . . . . . . . . . . . . . . .
[1]1hnd.a . . * . . . . . . . . . . . . . . . . . . . . . . .
[1]1hnh.a . . . . . * . . . . . . * . . . . . . . * . . . . .
[1]1hnj.a . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]1mzs.a . . * . . ocs * . . . . . . . . . . . . . . . . . . .
[1]2eft.a . . * . . . . . . . . . . . . . . . . . . . . . . .
[1]4z8d.a . . * . . . . . . . . . . . . . . . . . . . . . . .
[1]5bnm.a . . . . . . * . . . . . . . . . . . . . . . . . . .
[1]5bnr.a . . . . . . * . . . . . . . . . . . . . . . . . . .
[1]5bns.a . . * . . . . . . . . . . . . . . . . . . . . . . .
[2]1ebl.a . . * * . . . . . . . . * . . . . . . . . . . . . .
[2]3il9.a . . . * . csw . . . . . . . . . . . . . . . . * . . .
[3]5bnm.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
1hn9.a is apo
1hnd.a:coa
1hnh.a:coa
1hnj.a:mlc
1mzs.a:669
2eft.a:coa
4z8d.a:4lb
5bnm.a:4vk
5bnr.a:4vl
5bns.a:4vm
1ebl.a:coa
3il9.a is apo
5bnm.b:pg4
[1] 1hn9.a
-
3.8 3.5 3.3 0.8 3.4 0.2 0.4 0.2 2.3 2.1 - 0.2
[1] 1hnd.a -
0.3
0.2 0.1 0.8 0.2 0.5 3.0 0.4 1.0 2.3 - 0.2
[1] 1hnh.a - 0.4
0.2
0.1 0.7 0.2 0.1 2.2 0.3 1.1 2.0 - 0.3
[1] 1hnj.a - 0.3 0.2
0
0.5 0 0.1 1.7 0.3 1.1 2.0 - 0.2
[1] 1mzs.a - 4.1 3.6 3.3
0.1
3.5 0.4 1.2 0.7 3.9 3.1 - 0.7
[1] 2eft.a - 0.2 0.2 0 0.5
0
0.3 2.1 0.3 0.8 2.4 - 0.2
[1] 4z8d.a - 0.7 0.6 0.5 0.9 0.5
0
1.8 0.3 1.4 2.5 - 0.2
[1] 5bnm.a - 3.9 3.6 3.4 1.0 3.6 0.3
0.1
0.2 2.8 2.3 - 0
[1] 5bnr.a - 4.3 4.3 4.2 1.0 4.3 0.6 1.6
0
3.5 3.5 - 0.1
[1] 5bns.a - 0.7 0.8 0.6 0.6 0.6 0.2 2.2 0.1
0
1.8 - 0.2
[2] 1ebl.a - 5.4 5.3 5.2 2.2 5.0 2.3 3.7 0.7 3.4
0.5
- 1.0
[2] 3il9.a - 3.2 2.9 2.4 2.5 2.0 2.0 4.1 0.9 1.3 1.7
-
1.1
[3] 5bnm.b - 6.7 6.7 5.8 4.0 5.2 2.7 4.9 3.0 4.9 4.8 -
0
[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
1hn9.a
1hnd.a
1hnh.a
1hnj.a
1mzs.a
2eft.a
4z8d.a
5bnm.a
5bnr.a
5bns.a
1ebl.a
3il9.a
5bnm.b
[1] 1hn9.a
0
.23 .20 .18 .17 .19 .19 .07 .13 .18 .37 .33 .41
[1] 1hnd.a .23
0
.07 .06 .27 .08 .10 .26 .23 .12 .30 .24 .47
[1] 1hnh.a .20 .07
0
.03 .23 .10 .10 .21 .23 .12 .29 .20 .44
[1] 1hnj.a .18 .06 .03
0
.23 .07 .07 .21 .23 .10 .29 .20 .43
[1] 1mzs.a .17 .27 .23 .23
0
.22 .24 .17 .20 .23 .25 .34 .35
[1] 2eft.a .19 .08 .10 .07 .22
0
.07 .22 .21 .08 .29 .26 .45
[1] 4z8d.a .19 .10 .10 .07 .24 .07
0
.23 .22 .12 .32 .23 .42
[1] 5bnm.a .07 .26 .21 .21 .17 .22 .23
0
.10 .19 .33 .30 .38
[1] 5bnr.a .13 .23 .23 .23 .20 .21 .22 .10
0
.18 .34 .34 .39
[1] 5bns.a .18 .12 .12 .10 .23 .08 .12 .19 .18
0
.29 .26 .43
[2] 1ebl.a .37 .30 .29 .29 .25 .29 .32 .33 .34 .29
0
.23 .28
[2] 3il9.a .33 .24 .20 .20 .34 .26 .23 .30 .34 .26 .23
0
.35
[3] 5bnm.b .41 .47 .44 .43 .35 .45 .42 .38 .39 .43 .28 .35
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 1.1 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
1hn9.a
1hnd.a
1hnh.a
1hnj.a
1mzs.a
2eft.a
4z8d.a
5bnm.a
5bnr.a
5bns.a
1ebl.a
3il9.a
5bnm.b
[1] 1hn9.a
0
0.5 0.4 0.4 0.3 0.4 0.5 0.3 0.3 0.3 0.7 0.7 0.5
[1] 1hnd.a 0.5
0
0.2 0.1 0.4 0.3 0.4 0.6 0.4 0.5 0.7 0.5 0.6
[1] 1hnh.a 0.4 0.2
0
0.2 0.3 0.3 0.4 0.5 0.4 0.5 0.7 0.5 0.6
[1] 1hnj.a 0.4 0.1 0.2
0
0.3 0.2 0.3 0.5 0.4 0.4 0.7 0.5 0.6
[1] 1mzs.a 0.3 0.4 0.3 0.3
0
0.4 0.5 0.5 0.3 0.5 0.6 0.5 0.6
[1] 2eft.a 0.4 0.3 0.3 0.2 0.4
0
0.3 0.5 0.4 0.4 0.8 0.6 0.6
[1] 4z8d.a 0.5 0.4 0.4 0.3 0.5 0.3
0
0.6 0.5 0.5 0.9 0.7 0.6
[1] 5bnm.a 0.3 0.6 0.5 0.5 0.5 0.5 0.6
0
0.4 0.4 0.8 0.8 0.6
[1] 5bnr.a 0.3 0.4 0.4 0.4 0.3 0.4 0.5 0.4
0
0.4 0.6 0.6 0.5
[1] 5bns.a 0.3 0.5 0.5 0.4 0.5 0.4 0.5 0.4 0.4
0
0.8 0.7 0.6
[2] 1ebl.a 0.7 0.7 0.7 0.7 0.6 0.8 0.9 0.8 0.6 0.8
0
0.5 0.8
[2] 3il9.a 0.7 0.5 0.5 0.5 0.5 0.6 0.7 0.8 0.6 0.7 0.5
0
0.6
[3] 5bnm.b 0.5 0.6 0.6 0.6 0.6 0.6 0.6 0.6 0.5 0.6 0.8 0.6
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
1hn9.a
1hnd.a
1hnh.a
1hnj.a
1mzs.a
2eft.a
4z8d.a
5bnm.a
5bnr.a
5bns.a
1ebl.a
3il9.a
5bnm.b
[1] 1hn9.a
0
1.0 0.9 0.8 0.7 0.8 1.0 0.7 0.7 1.1 1.1 1.4 1.1
[1] 1hnd.a 1.0
0
0.3 0.8 1.1 1.0 1.1 1.4 1.0 1.2 1.2 1.5 1.6
[1] 1hnh.a 0.9 0.3
0
0.6 1.0 1.0 1.0 1.2 1.0 1.2 1.2 1.4 1.5
[1] 1hnj.a 0.8 0.8 0.6
0
0.8 0.9 0.9 1.3 0.9 1.1 1.4 1.5 1.5
[1] 1mzs.a 0.7 1.1 1.0 0.8
0
1.0 1.1 1.2 0.8 1.2 1.4 1.7 1.5
[1] 2eft.a 0.8 1.0 1.0 0.9 1.0
0
0.7 1.1 1.0 0.9 1.6 1.8 1.6
[1] 4z8d.a 1.0 1.1 1.0 0.9 1.1 0.7
0
1.2 1.0 1.0 1.6 1.7 1.6
[1] 5bnm.a 0.7 1.4 1.2 1.3 1.2 1.1 1.2
0
1.1 1.2 1.6 1.7 1.6
[1] 5bnr.a 0.7 1.0 1.0 0.9 0.8 1.0 1.0 1.1
0
1.1 1.4 1.6 1.3
[1] 5bns.a 1.1 1.2 1.2 1.1 1.2 0.9 1.0 1.2 1.1
0
1.8 1.9 1.8
[2] 1ebl.a 1.1 1.2 1.2 1.4 1.4 1.6 1.6 1.6 1.4 1.8
0
1.3 1.5
[2] 3il9.a 1.4 1.5 1.4 1.5 1.7 1.8 1.7 1.7 1.6 1.9 1.3
0
1.7
[3] 5bnm.b 1.1 1.6 1.5 1.5 1.5 1.6 1.6 1.6 1.3 1.8 1.5 1.7
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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