If you see this message after the page is completely loaded, then JavaScript is not supported or disabled in your browser. Please consider enabling JavaScript for this site.

CAN1_RAT_24_356

Calpain-1 catalytic subunit [Peptidase C2 family]

Composition of the binding site

Protein chains monomer [domain annotation]
A1 (CAN1_RAT):D: Calpain catalytic (72, 109, 110, 112:116, 206:210, 212, 251:253, 260, 261, 271:273, 298, 300, 347)72, 109, 110, 112:116, 206:210, 212, 251:253, 260, 261, 271:273, 298, 300, 347
Metals (Me):Ca

Full PDB list

1kxr, 1tl9, 1tlo, 2g8e, 2g8j, 2nqg, 2nqi, 2r9c, 2r9f; 1qxp (unprocessed)

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1 Me
E
7
2
Q
1
0
9
G
1
1
0
L
1
1
2
G
1
1
3
D
1
1
4
C
1
1
5
W
1
1
6
S
2
0
6
G
2
0
7
G
2
0
8
C
2
0
9
T
2
1
0
E
2
1
2
S
2
5
1
I
2
5
2
N
2
5
3
L
2
6
0
E
2
6
1
G
2
7
1
H
2
7
2
A
2
7
3
W
2
9
8
E
3
0
0
K
3
4
7
[1]1kxr.a none . . . . . . S . . . . . . . . . . . . . . . . . . Ca
[1]1tl9.a aceLLar730 . . . . . . . . . . . . . . . . . . . . . . . . . Ca
[1]1tlo.a e6425 . . . . . . * . . . . . . . . . . . . . . . . . . Ca
[1]2g8e.a 0m624 . . . . . . * . . . . . . . . . . . . . . . . . . Ca
[1]2g8j.a d7g35 . . . . . . * . . . . . . . . . . . . . . . . . . Ca
[1]2nqg.a nqg44 . . . . . . * . . . . . . . . . . . . . . . . . . Ca
[1]2nqi.a nqi43 . . . . . . * . . . . . . . . . . . . . . . . . . Ca
[1]2r9c.a grd40 . . . . . . . . . . . . . . . . . . . . . . . . . Ca
[1]2r9f.a k2z37 . . . . . . * . . . . . . . . . . . . . . . . . . Ca

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
E
7
2
Q
1
0
9
G
1
1
0
L
1
1
2
G
1
1
3
D
1
1
4
C
1
1
5
W
1
1
6
S
2
0
6
G
2
0
7
G
2
0
8
C
2
0
9
T
2
1
0
E
2
1
2
S
2
5
1
I
2
5
2
N
2
5
3
L
2
6
0
E
2
6
1
G
2
7
1
H
2
7
2
A
2
7
3
W
2
9
8
E
3
0
0
K
3
4
7
[1]1kxr.a . . . . . . S . . . . . . . . . * . * . . . . . . Ca
[1]1tl9.a . . . . . . * . . . . . . . . . . . * . . . . . . Ca
[1]1tlo.a . . . . . . * . . . . . . . . . . . . . . . . . . Ca
[1]2g8e.a . . . . . . * . . . . . . . . . . . * . . . . . . Ca
[1]2g8j.a . . . . . . * . . . . . . . . . . . . . . . . . . Ca
[1]2nqg.a . . . . . . * . . . . . . . . . . . . . . . . . . Ca
[1]2nqi.a . . . . . . * . . . . . . . . . . . . . . . . . . Ca
[1]2r9c.a . . . . . . * . . . . . . . . . . . . . . . . . . Ca
[1]2r9f.a . . . . . . * . . . . . . . . . . . . . . . . . . Ca

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

zoom: [−] [+]; [view as image]; [download as text]

pocketligand
≥10
9
8
7
6
5
4
3
2
1
0
1kxr.a is apo
1tl9.a:aceLLar7
1tlo.a:e64
2g8e.a:0m6
2g8j.a:d7g
2nqg.a:nqg
2nqi.a:nqi
2r9c.a:grd
2r9f.a:k2z
[1] 1kxr.a
-
0.3 0.7 0.4 1.8 2.2 1.6 1.7 1.5
[1] 1tl9.a -
0.4
0.8 0.6 1.3 1.2 1.2 1.4 0.8
[1] 1tlo.a - 0.4
0.9
0.4 0.9 0.6 0.7 1.2 0.7
[1] 2g8e.a - 0.5 0.8
0.6
1.3 1.4 1.5 1.6 1.0
[1] 2g8j.a - 0.4 0.7 0.6
0.4
0.8 0.7 0.4 0.3
[1] 2nqg.a - 0.4 0.9 0.4 0.5
0.5
0.5 0.8 0.6
[1] 2nqi.a - 0.4 0.6 0.4 0.5 0.5
0.6
0.7 0.6
[1] 2r9c.a - 0.4 0.7 0.6 0.4 0.8 0.6
0.4
0.3
[1] 2r9f.a - 0.4 1.0 0.9 0.4 1.1 0.6 0.4
0.3
[Pocket-ligand steric clashes matrix]

Pocket clash dissimilarity (1 cluster)

Pockets (x) vs pockets (y) colored by ligand clash profile difference

zoom: [−] [+]; [view as image]; [download as text]

pocketpocket
≥1.
.9
.8
.7
.6
.5
.4
.3
.2
.1
.0
1kxr.a
1tl9.a
1tlo.a
2g8e.a
2g8j.a
2nqg.a
2nqi.a
2r9c.a
2r9f.a
[1] 1kxr.a
0
.10 .09 .09 .12 .10 .10 .12 .13
[1] 1tl9.a .10
0
.04 .02 .06 .07 .05 .06 .07
[1] 1tlo.a .09 .04
0
.05 .05 .03 .03 .05 .05
[1] 2g8e.a .09 .02 .05
0
.05 .06 .05 .05 .07
[1] 2g8j.a .12 .06 .05 .05
0
.03 .02 0 .01
[1] 2nqg.a .10 .07 .03 .06 .03
0
.02 .03 .03
[1] 2nqi.a .10 .05 .03 .05 .02 .02
0
.02 .03
[1] 2r9c.a .12 .06 .05 .05 0 .03 .02
0
.01
[1] 2r9f.a .13 .07 .05 .07 .01 .03 .03 .01
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 1.5 Å)

Pockets (x) vs pockets (y) colored by RMSD of site residue backbone atoms

zoom: [−] [+]; [view as image]; [download as text]

pocketpocket
≥10 Å
9 Å
8 Å
7 Å
6 Å
5 Å
4 Å
3 Å
2 Å
1 Å
0 Å
1kxr.a
1tl9.a
1tlo.a
2g8e.a
2g8j.a
2nqg.a
2nqi.a
2r9c.a
2r9f.a
[1] 1kxr.a
0
0.9 0.8 1.0 2.8 2.6 2.8 2.8 2.8
[1] 1tl9.a 0.9
0
0.6 0.3 2.3 2.2 2.4 2.3 2.3
[1] 1tlo.a 0.8 0.6
0
0.6 2.3 2.1 2.3 2.3 2.3
[1] 2g8e.a 1.0 0.3 0.6
0
2.3 2.2 2.3 2.3 2.3
[1] 2g8j.a 2.8 2.3 2.3 2.3
0
0.4 0.2 0.2 0.3
[1] 2nqg.a 2.6 2.2 2.1 2.2 0.4
0
0.4 0.3 0.3
[1] 2nqi.a 2.8 2.4 2.3 2.3 0.2 0.4
0
0.3 0.3
[1] 2r9c.a 2.8 2.3 2.3 2.3 0.2 0.3 0.3
0
0.1
[1] 2r9f.a 2.8 2.3 2.3 2.3 0.3 0.3 0.3 0.1
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 1.0 Å)

Pockets (x) vs pockets (y) colored by RMSD of all site residue atoms

zoom: [−] [+]; [view as image]; [download as text]

pocketpocket
≥10 Å
9 Å
8 Å
7 Å
6 Å
5 Å
4 Å
3 Å
2 Å
1 Å
0 Å
1kxr.a
1tl9.a
1tlo.a
2g8e.a
2g8j.a
2nqg.a
2nqi.a
2r9c.a
2r9f.a
[1] 1kxr.a
0
1.5 1.3 1.3 3.8 3.6 3.9 3.6 3.8
[1] 1tl9.a 1.5
0
1.2 0.9 3.5 3.3 3.5 3.2 3.5
[1] 1tlo.a 1.3 1.2
0
0.8 3.3 3.2 3.5 3.1 3.4
[1] 2g8e.a 1.3 0.9 0.8
0
3.4 3.2 3.5 3.1 3.4
[1] 2g8j.a 3.8 3.5 3.3 3.4
0
0.6 0.6 0.8 0.5
[1] 2nqg.a 3.6 3.3 3.2 3.2 0.6
0
0.7 0.9 0.8
[1] 2nqi.a 3.9 3.5 3.5 3.5 0.6 0.7
0
0.9 0.7
[1] 2r9c.a 3.6 3.2 3.1 3.1 0.8 0.9 0.9
0
0.7
[1] 2r9f.a 3.8 3.5 3.4 3.4 0.5 0.8 0.7 0.7
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

L C X E | Background Color: | Anaglyph Stereo:

loading...