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ACT3_STRCO_2_261

Putative ketoacyl reductase [Short-chain dehydrogenases/reductases (SDR) family]

Composition of the binding site

Protein chains monomer
A1 (ACT3_STRCO):94, 144:146, 149, 151, 157, 188, 189, 194, 198, 201, 202, 217, 220, 221, 25894, 144:146, 149, 151, 157, 188, 189, 194, 198, 201, 202, 217, 220, 221, 258
Cofactors (cF):nap/ndp

Full PDB list

1w4z, 1x7g, 1x7h, 1xr3, 2rh4, 2rhc, 2rhr, 3csd, 3qrw, 3ri3, 4dbz, 4dc0, 4dc1 (redundant Pocketome entry)

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1 cF
P
9
4
S
1
4
4
T
1
4
5
G
1
4
6
Q
1
4
9
V
1
5
1
Y
1
5
7
G
1
8
8
F
1
8
9
M
1
9
4
V
1
9
8
I
2
1
7
R
2
2
0
V
2
2
1
L
2
5
8
[1]2rhc.b none . . . . . . . . . . . . . . . nap
[1]3qrw.b none L . . . . . . . . . . . . . . ndp
[1]4dbz.b none . . . . . L . . . . . . . . . ndp
[1]4dc1.b none . . . . . . . . . . . . . . . ndp
[2]1xr3.a isz10 . . . . . . . . . . . . . . . nap
[2]2rhc.a emo20 . . . . . . . . . . . . . . . nap
[2]4dc0.b none . . . . . . . . W . . . . . . ndp
[3]2rhr.a emo,emo40 L . . . . . . . . . . . . . . ndp

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
P
9
4
S
1
4
4
T
1
4
5
G
1
4
6
Q
1
4
9
V
1
5
1
Y
1
5
7
G
1
8
8
F
1
8
9
M
1
9
4
V
1
9
8
H
2
0
1
Y
2
0
2
I
2
1
7
R
2
2
0
V
2
2
1
L
2
5
8
[1]2rhc.b . . . . . . . . * . . . . . * . . nap
[1]3qrw.b L . . . . . . . * . . . . . * . . ndp
[1]4dbz.b . . . . . L . . * . . . . . * . . ndp
[1]4dc1.b . . . . . . . . * . . . F . * . . ndp
[2]1xr3.a . . . . . . . . * . . . . . . . . nap
[2]2rhc.a . . . . . . . . * * . . . . . . . nap
[2]4dc0.b . . . . * . . . W . . . . . * . . ndp
[3]2rhr.a L . . . . . . . . . . . . . . . . ndp

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
2rhc.b is apo
3qrw.b is apo
4dbz.b is apo
4dc1.b is apo
1xr3.a:isz
2rhc.a:emo
4dc0.b is apo
2rhr.a:emo
[1] 2rhc.b
-
- - - 0.1 1.2 - 7.5
[1] 3qrw.b -
-
- - 0 0.8 - 7.5
[1] 4dbz.b - -
-
- 0.3 1.8 - 8.5
[1] 4dc1.b - - -
-
0.1 0.8 - 6.5
[2] 1xr3.a - - - -
0
0.1 - 3.2
[2] 2rhc.a - - - - 0.1
0
- 4.3
[2] 4dc0.b - - - - 0.5 0.8
-
6.6
[3] 2rhr.a - - - - 0.1 0.6 -
0.1
[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
2rhc.b
3qrw.b
4dbz.b
4dc1.b
1xr3.a
2rhc.a
4dc0.b
2rhr.a
[1] 2rhc.b
0
.12 .14 .11 .26 .28 .31 .46
[1] 3qrw.b .12
0
.11 .13 .25 .26 .29 .44
[1] 4dbz.b .14 .11
0
.17 .33 .36 .36 .51
[1] 4dc1.b .11 .13 .17
0
.20 .22 .22 .38
[2] 1xr3.a .26 .25 .33 .20
0
.08 .21 .20
[2] 2rhc.a .28 .26 .36 .22 .08
0
.24 .27
[2] 4dc0.b .31 .29 .36 .22 .21 .24
0
.40
[3] 2rhr.a .46 .44 .51 .38 .20 .27 .40
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 1.9 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
2rhc.b
3qrw.b
4dbz.b
4dc1.b
1xr3.a
2rhc.a
4dc0.b
2rhr.a
[1] 2rhc.b
0
0.7 0.8 0.8 2.1 2.0 0.9 1.4
[1] 3qrw.b 0.7
0
0.4 0.3 2.0 1.9 0.7 1.3
[1] 4dbz.b 0.8 0.4
0
0.5 2.0 2.0 0.7 1.4
[1] 4dc1.b 0.8 0.3 0.5
0
1.8 1.8 0.5 1.2
[2] 1xr3.a 2.1 2.0 2.0 1.8
0
0.2 1.9 0.9
[2] 2rhc.a 2.0 1.9 2.0 1.8 0.2
0
1.9 0.8
[2] 4dc0.b 0.9 0.7 0.7 0.5 1.9 1.9
0
1.4
[3] 2rhr.a 1.4 1.3 1.4 1.2 0.9 0.8 1.4
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 0.9 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
2rhc.b
3qrw.b
4dbz.b
4dc1.b
1xr3.a
2rhc.a
4dc0.b
2rhr.a
[1] 2rhc.b
0
1.4 1.5 1.4 3.3 3.1 1.6 2.2
[1] 3qrw.b 1.4
0
0.7 0.7 3.0 3.0 1.1 2.0
[1] 4dbz.b 1.5 0.7
0
0.8 3.1 3.1 1.1 2.2
[1] 4dc1.b 1.4 0.7 0.8
0
2.8 2.7 1.0 1.9
[2] 1xr3.a 3.3 3.0 3.1 2.8
0
1.2 2.8 2.0
[2] 2rhc.a 3.1 3.0 3.1 2.7 1.2
0
2.8 2.1
[2] 4dc0.b 1.6 1.1 1.1 1.0 2.8 2.8
0
1.8
[3] 2rhr.a 2.2 2.0 2.2 1.9 2.0 2.1 1.8
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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