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D14_ORYSJ_50_318

Strigolactone esterase D14 [AB hydrolase superfamily]

Composition of the binding site

Protein chains monomer
A1 (D14_ORYSJ):77, 78, 147, 148, 151, 176, 186, 194, 205, 209, 212, 241, 244, 245, 269, 270, 29777, 78, 147, 148, 151, 176, 186, 194, 205, 209, 212, 241, 244, 245, 269, 270, 297

Full PDB list

3vxk, 3w04, 3w05, 3wio, 4ih9, 4iha, 5dj5 (redundant Pocketome entry)

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1
F
7
8
S
1
4
7
V
1
4
8
M
1
5
1
F
1
7
6
F
1
8
6
V
1
9
4
W
2
0
5
Y
2
0
9
C
2
4
1
V
2
4
4
F
2
4
5
V
2
6
9
S
2
7
0
H
2
9
7
[1]3w04.b none . . . . . . . . . . . . . . .
[1]3w05.b pms10 . * . . . . . . . . . . . . .
[1]3wio.a h3m8 . . . . . . . . . . . . . . .
[1]4iha.b opl9 . * . . . . . . . . . . . . .
[1]5dj5.a gr222 . . . . . . . . . . . . . . .

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
G
7
7
F
7
8
S
1
4
7
V
1
4
8
M
1
5
1
F
1
7
6
F
1
8
6
V
1
9
4
W
2
0
5
Y
2
0
9
L
2
1
2
C
2
4
1
V
2
4
4
F
2
4
5
V
2
6
9
S
2
7
0
H
2
9
7
[1]3w04.b . . * . . . . . . . . . . . . . .
[1]3w05.b . . * . . . . . . . . . . . . . .
[1]3wio.a . . * . . . . . . . . . . * . . .
[1]4iha.b . . * . . . . . . . . . . . . . .
[1]5dj5.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
3w04.b is apo
3w05.b:pms
3wio.a:h3m
4iha.b:opl
5dj5.a:gr2
[1] 3w04.b
-
0.7 0 0.8 0.3
[1] 3w05.b -
0.6
0 0.5 0.1
[1] 3wio.a - 1.5
0
0.7 0.1
[1] 4iha.b - 0.6 0
0.4
0.2
[1] 5dj5.a - 0.6 0 0.6
0.1
[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
3w04.b
3w05.b
3wio.a
4iha.b
5dj5.a
[1] 3w04.b
0
.02 .08 .01 .03
[1] 3w05.b .02
0
.05 .01 .02
[1] 3wio.a .08 .05
0
.06 .05
[1] 4iha.b .01 .01 .06
0
.02
[1] 5dj5.a .03 .02 .05 .02
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

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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
3w04.b
3w05.b
3wio.a
4iha.b
5dj5.a
[1] 3w04.b
0
0.3 0.4 0.2 0.4
[1] 3w05.b 0.3
0
0.3 0.3 0.4
[1] 3wio.a 0.4 0.3
0
0.3 0.3
[1] 4iha.b 0.2 0.3 0.3
0
0.3
[1] 5dj5.a 0.4 0.4 0.3 0.3
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 0.3 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
3w04.b
3w05.b
3wio.a
4iha.b
5dj5.a
[1] 3w04.b
0
0.9 0.8 0.7 0.8
[1] 3w05.b 0.9
0
0.6 0.8 0.8
[1] 3wio.a 0.8 0.6
0
0.8 0.7
[1] 4iha.b 0.7 0.8 0.8
0
0.5
[1] 5dj5.a 0.8 0.8 0.7 0.5
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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