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ACTPC_ACTFR_1_179

DELTA-actitoxin-Afr1a [Actinoporin family. Sea anemone subfamily]

Composition of the binding site

Protein chains monomer [domain annotation]
A1 (ACTPC_ACTFR):R: Trp-rich region (105, 107:114, 116)
53, 54, 82:85, 87, 130, 133, 134, 137:139, 142, 144
53, 54, 82:85, 87, 105, 107:114, 116, 130, 133, 134, 137:139, 142, 144

Full PDB list

3lim, 3vwi, 3w9p, 3zwg, 3zwj, 4tsl, 4tsn, 4tso, 4tsp, 4tsq, 4tsy, 4wdc, 5bpg, 5gwf (redundant Pocketome entry)

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1
R
5
3
S
5
4
A
8
3
T
8
4
G
8
5
V
8
7
S
1
0
5
P
1
0
7
Y
1
0
8
D
1
0
9
N
1
1
1
W
1
1
2
Y
1
1
3
S
1
1
4
W
1
1
6
Q
1
3
0
Y
1
3
3
E
1
3
4
Y
1
3
7
Y
1
3
8
H
1
3
9
P
1
4
2
R
1
4
4
[1]3lim.a lda,lda30 . . . . . . . . . . . . . . . . . . . . . . .
[1]3w9p.b none . . . . . . . . . . . . . . . . . . . . . . .
[1]4tsn.a pc,pc,pc33 . . . . . . . . . . . . . . . . . . . . . . .
[1]4tsn.b pc,pc22 . . . . . . . . . . . . . . . . . . . . . . .
[1]4tsn.c pc11 . . . . . . . . . . . . . . . . . . . . . . .
[1]4tso.a hxg,hxg,hxg90 . . . . . . . . . . . . . . . . . . . . . . .
[1]4tsp.a hxg,hxg60 . . . . . . . . . . . . . . . . . . . . . . .
[1]4tsq.a hxg,hxg,hxg,hxg,pc131 . . . . . . . . . . . . . . . . . . . . . . .
[1]4tsq.b hxg,hxg,hxg,hxg120 . . . . . . . . . . . . . . . . . . . . . . .
[1]4tsq.c hxg,hxg,pc71 . . . . . . . . . . . . . . . . . . . . . . .
[1]4tsy.a hxj,hxj60 . . . . . . . . . . . . . . . . . . . . . . .

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
R
5
3
S
5
4
V
8
2
A
8
3
T
8
4
G
8
5
V
8
7
S
1
0
5
P
1
0
7
Y
1
0
8
D
1
0
9
Y
1
1
0
N
1
1
1
W
1
1
2
Y
1
1
3
S
1
1
4
W
1
1
6
Q
1
3
0
Y
1
3
3
E
1
3
4
Y
1
3
7
Y
1
3
8
H
1
3
9
P
1
4
2
R
1
4
4
[1]3lim.a . . . . . . . . . . . . . . . . . . . . . . . . .
[1]3w9p.b . . . . * . . . . . . . . * . . . . . . . . . . .
[1]4tsn.a . . . . . . . . . . . . . . . . . . . . . . . . .
[1]4tsn.b . . . . . . . . . . . . . . . . . . . . . . . . .
[1]4tsn.c . . . . . . . . . . . . . * . . . . . . . . . . .
[1]4tso.a . . . . . . . . . . . . . . . . . . . . . . . . .
[1]4tsp.a . . . . . . . . . . . . . . . . . . . . . . . . .
[1]4tsq.a . . . . . . . . . . . . . . . . . . . . . . . . .
[1]4tsq.b . . . . . . . . . . . . . . . . . . . . . . . . .
[1]4tsq.c . . . . . . . . . . . . . * . . . . . . . . . . .
[1]4tsy.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
3lim.a:lda
3w9p.b is apo
4tsn.a:pc
4tsn.b:pc
4tsn.c:pc
4tso.a:hxg
4tsp.a:hxg
4tsq.a:hxg,pc
4tsq.b:hxg
4tsq.c:hxg,pc
4tsy.a:hxj
[1] 3lim.a
0
- 0.1 0.1 0 0.6 0.4 1.0 0.6 0.2 0.3
[1] 3w9p.b 0.4
-
1.7 0.3 0.1 2.1 1.6 2.1 2.4 0.8 2.6
[1] 4tsn.a 0.3 -
0
0 0 0.4 0.5 0.2 0.3 0.2 0.1
[1] 4tsn.b 0.5 - 0.2
0
0 0.4 0.4 0.1 0.1 0.2 0.1
[1] 4tsn.c 0.6 - 0.6 0
0
0.7 2.4 0.5 0.3 0.1 1.4
[1] 4tso.a 0.8 - 0.4 0 0.1
0.1
0.3 0.4 0.5 0.2 0.4
[1] 4tsp.a 0.6 - 0.2 0 0 0.2
0.1
0.6 0.5 0.3 0
[1] 4tsq.a 0.8 - 0.2 0 0 0.6 0.3
0
0.1 0.1 0.1
[1] 4tsq.b 0.8 - 0.2 0.1 0 0.4 0.2 0.1
0
0.3 0.1
[1] 4tsq.c 3.0 - 0.2 0.2 0.1 2.4 1.9 1.5 1.7
0
0.7
[1] 4tsy.a 0.9 - 0.1 0 0 0.2 0 0.2 0.1 0.2
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
3lim.a
3w9p.b
4tsn.a
4tsn.b
4tsn.c
4tso.a
4tsp.a
4tsq.a
4tsq.b
4tsq.c
4tsy.a
[1] 3lim.a
0
.10 .05 .06 .11 .06 .07 .05 .06 .15 .05
[1] 3w9p.b .10
0
.12 .13 .10 .13 .15 .13 .13 .10 .13
[1] 4tsn.a .05 .12
0
.05 .12 .07 .07 .04 .06 .14 .05
[1] 4tsn.b .06 .13 .05
0
.09 .05 .04 .02 .01 .14 .02
[1] 4tsn.c .11 .10 .12 .09
0
.12 .13 .09 .10 .09 .10
[1] 4tso.a .06 .13 .07 .05 .12
0
.06 .05 .06 .14 .05
[1] 4tsp.a .07 .15 .07 .04 .13 .06
0
.04 .04 .17 .04
[1] 4tsq.a .05 .13 .04 .02 .09 .05 .04
0
.02 .13 .02
[1] 4tsq.b .06 .13 .06 .01 .10 .06 .04 .02
0
.15 .02
[1] 4tsq.c .15 .10 .14 .14 .09 .14 .17 .13 .15
0
.14
[1] 4tsy.a .05 .13 .05 .02 .10 .05 .04 .02 .02 .14
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 0.9 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
3lim.a
3w9p.b
4tsn.a
4tsn.b
4tsn.c
4tso.a
4tsp.a
4tsq.a
4tsq.b
4tsq.c
4tsy.a
[1] 3lim.a
0
0.3 0.4 0.4 0.5 1.0 0.8 0.5 0.4 0.4 0.4
[1] 3w9p.b 0.3
0
0.4 0.4 0.4 0.9 0.7 0.4 0.3 0.5 0.4
[1] 4tsn.a 0.4 0.4
0
0.2 0.5 0.8 0.7 0.3 0.2 0.6 0.3
[1] 4tsn.b 0.4 0.4 0.2
0
0.4 0.8 0.6 0.2 0.2 0.5 0.3
[1] 4tsn.c 0.5 0.4 0.5 0.4
0
0.9 0.7 0.5 0.4 0.5 0.5
[1] 4tso.a 1.0 0.9 0.8 0.8 0.9
0
0.4 0.7 0.8 0.9 0.9
[1] 4tsp.a 0.8 0.7 0.7 0.6 0.7 0.4
0
0.5 0.7 0.8 0.7
[1] 4tsq.a 0.5 0.4 0.3 0.2 0.5 0.7 0.5
0
0.2 0.6 0.3
[1] 4tsq.b 0.4 0.3 0.2 0.2 0.4 0.8 0.7 0.2
0
0.5 0.3
[1] 4tsq.c 0.4 0.5 0.6 0.5 0.5 0.9 0.8 0.6 0.5
0
0.6
[1] 4tsy.a 0.4 0.4 0.3 0.3 0.5 0.9 0.7 0.3 0.3 0.6
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
3lim.a
3w9p.b
4tsn.a
4tsn.b
4tsn.c
4tso.a
4tsp.a
4tsq.a
4tsq.b
4tsq.c
4tsy.a
[1] 3lim.a
0
0.9 0.7 0.6 1.3 1.1 1.0 0.6 0.6 0.8 0.8
[1] 3w9p.b 0.9
0
0.9 1.0 1.2 1.2 1.2 1.0 0.9 1.2 1.1
[1] 4tsn.a 0.7 0.9
0
0.5 1.1 1.0 0.9 0.6 0.6 1.0 0.7
[1] 4tsn.b 0.6 1.0 0.5
0
1.2 0.8 0.8 0.4 0.4 0.9 0.6
[1] 4tsn.c 1.3 1.2 1.1 1.2
0
1.5 1.4 1.3 1.2 1.5 1.3
[1] 4tso.a 1.1 1.2 1.0 0.8 1.5
0
0.5 0.7 0.9 1.1 1.0
[1] 4tsp.a 1.0 1.2 0.9 0.8 1.4 0.5
0
0.7 0.8 1.0 0.9
[1] 4tsq.a 0.6 1.0 0.6 0.4 1.3 0.7 0.7
0
0.4 0.8 0.6
[1] 4tsq.b 0.6 0.9 0.6 0.4 1.2 0.9 0.8 0.4
0
0.8 0.6
[1] 4tsq.c 0.8 1.2 1.0 0.9 1.5 1.1 1.0 0.8 0.8
0
0.9
[1] 4tsy.a 0.8 1.1 0.7 0.6 1.3 1.0 0.9 0.6 0.6 0.9
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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