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A1HB2_LOXIN_17_302

Phospholipase D LiSicTox-alphaIA1bii [Arthropod phospholipase D family. Class II subfamily]

Composition of the binding site

Protein chains monomer [domain annotation]
A1 (A1HB2_LOXIN):D: GDPD (245, 247, 267)
34, 54, 56, 70, 114, 116, 155, 187, 189, 213
34, 54, 56, 70, 114, 116, 155, 187, 189, 213, 245, 247, 267
Metals (Me):Mg

Full PDB list

3rlg, 4rw3, 4rw5

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1 Me
H
3
4
E
5
4
D
5
6
H
7
0
D
1
1
4
K
1
1
6
S
1
5
5
S
1
8
9
Y
2
4
5
W
2
4
7
M
2
6
7
[1]3rlg.a none A . . . . . . . . . . Mg
[1]4rw3.a ipd16 . . . . . . . . . . . Mg
[1]4rw5.a oca10 A . . . . . . . . . . Mg

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 Me
H
3
4
E
5
4
D
5
6
H
7
0
D
1
1
4
K
1
1
6
S
1
5
5
D
1
8
7
S
1
8
9
S
2
1
3
Y
2
4
5
W
2
4
7
M
2
6
7
[1]3rlg.a A . . . . . . . . . . . . Mg
[1]4rw3.a . . . . . . . . . . . . . Mg
[1]4rw5.a A . . . . . . . . . . . . Mg

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
3rlg.a is apo
4rw3.a:ipd
4rw5.a:oca
[1] 3rlg.a
-
1.4 0.1
[1] 4rw3.a -
0.8
0.2
[1] 4rw5.a - 1.6
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
3rlg.a
4rw3.a
4rw5.a
[1] 3rlg.a
0
.06 .02
[1] 4rw3.a .06
0
.08
[1] 4rw5.a .02 .08
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 0.4 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
3rlg.a
4rw3.a
4rw5.a
[1] 3rlg.a
0
0.2 0.1
[1] 4rw3.a 0.2
0
0.2
[1] 4rw5.a 0.1 0.2
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 0.1 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
3rlg.a
4rw3.a
4rw5.a
[1] 3rlg.a
0
0.6 0.5
[1] 4rw3.a 0.6
0
0.4
[1] 4rw5.a 0.5 0.4
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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