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3SA3_NAJAT_22_81_SGC

Cytotoxin 3 [Snake three-finger toxin family. Short- chain subfamily. Type IA cytotoxin sub-subfamily]

Composition of the binding site

Protein chains monomer
A1 (3SA3_NAJAT):26, 27, 33, 36, 37, 39, 43, 45, 56:60, 64, 65, 7226, 27, 33, 36, 37, 39, 43, 45, 56:60, 64, 65, 72

Full PDB list

1h0j, 1xt3, 2bhi

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1
L
2
7
K
3
3
P
3
6
K
3
9
Y
4
3
K
5
6
R
5
7
G
5
8
C
5
9
P
6
4
K
6
5
Y
7
2
[1]1h0j.b sds17 . . . . . . . . . . . .
[1]1h0j.c none . . . . . . . . . . . .
[1]1xt3.a ids.sgn.ids.sgn.ids.sgn105 . . . . . . . . . . . .
[1]2bhi.b c10,sft78 . . . . . . . . . . . .

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
K
2
6
L
2
7
K
3
3
P
3
6
A
3
7
K
3
9
Y
4
3
M
4
5
K
5
6
R
5
7
G
5
8
C
5
9
I
6
0
P
6
4
K
6
5
Y
7
2
[1]1h0j.b . . . . . . . . . . . . . . . .
[1]1h0j.c . . . . . . . . . . . . . . . .
[1]1xt3.a . . . . . . . . . . . . . . . .
[1]2bhi.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
1h0j.b:sds
1h0j.c is apo
1xt3.a:ids.sgn.ids.sgn.ids.sgn
2bhi.b:c10,sft
[1] 1h0j.b
0
- 0.2 0.3
[1] 1h0j.c 0.3
-
0.3 0.3
[1] 1xt3.a 0 -
0.2
0.2
[1] 2bhi.b 0 - 0.5
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
1h0j.b
1h0j.c
1xt3.a
2bhi.b
[1] 1h0j.b
0
.04 .03 .02
[1] 1h0j.c .04
0
.04 .04
[1] 1xt3.a .03 .04
0
.04
[1] 2bhi.b .02 .04 .04
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 1.0 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
1h0j.b
1h0j.c
1xt3.a
2bhi.b
[1] 1h0j.b
0
0.5 0.4 0.4
[1] 1h0j.c 0.5
0
0.6 0.4
[1] 1xt3.a 0.4 0.6
0
0.4
[1] 2bhi.b 0.4 0.4 0.4
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
1h0j.b
1h0j.c
1xt3.a
2bhi.b
[1] 1h0j.b
0
0.9 1.1 1.1
[1] 1h0j.c 0.9
0
1.2 1.1
[1] 1xt3.a 1.1 1.2
0
0.7
[1] 2bhi.b 1.1 1.1 0.7
0
[Binding site full-atom RMSD matrix]







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[ENTRY 2D visualization]

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