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CNL_CLINE_2_149

Ricin B-like lectin

Composition of the binding site

Protein chains monomer
A1 (CNL_CLINE):21, 23:25, 34, 36, 39, 45, 47, 12421, 23:25, 34, 36, 39, 45, 47, 124

Full PDB list

3nbc, 3nbd, 3nbe

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1
D
2
1
T
2
3
G
2
4
S
2
5
I
3
4
H
3
6
N
3
9
Y
4
5
N
4
7
S
1
2
4
[1]3nbc.a lat23 . . . . . . . . . .
[1]3nbc.b none . . . . . . . . . .
[1]3nbd.a lbt23 . . . . . . . . . .
[1]3nbe.a dld33 . . . . . . . . . .

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

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PDB.ch
A1
D
2
1
T
2
3
G
2
4
S
2
5
I
3
4
H
3
6
N
3
9
Y
4
5
N
4
7
S
1
2
4
[1]3nbc.a . . . . . . . . . .
[1]3nbc.b . . . . . . . . . .
[1]3nbd.a . . . . . . . . . .
[1]3nbe.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
3nbc.a:lat
3nbc.b is apo
3nbd.a:lbt
3nbe.a:dld
[1] 3nbc.a
0
- 0 0
[1] 3nbc.b 0
-
0 0
[1] 3nbd.a 0 -
0
0
[1] 3nbe.a 0 - 0
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
3nbc.a
3nbc.b
3nbd.a
3nbe.a
[1] 3nbc.a
0
0 0 .01
[1] 3nbc.b 0
0
0 .01
[1] 3nbd.a 0 0
0
.01
[1] 3nbe.a .01 .01 .01
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 0.3 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
3nbc.a
3nbc.b
3nbd.a
3nbe.a
[1] 3nbc.a
0
0.2 0.2 0.3
[1] 3nbc.b 0.2
0
0.2 0.2
[1] 3nbd.a 0.2 0.2
0
0.2
[1] 3nbe.a 0.3 0.2 0.2
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 0.2 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
3nbc.a
3nbc.b
3nbd.a
3nbe.a
[1] 3nbc.a
0
0.3 0.3 0.3
[1] 3nbc.b 0.3
0
0.3 0.4
[1] 3nbd.a 0.3 0.3
0
0.3
[1] 3nbe.a 0.3 0.4 0.3
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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