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CPNS1_HUMAN_93_267

Calpain small subunit 1

Composition of the binding site

Protein chains monomer [domain annotation]
A1 (CPNS1_HUMAN):D: EF-hand 1
atypical (96:98, 100, 101, 103:105, 107, 108, 122:124)
D: EF-hand 2 (139, 164, 168, 171, 172)
D: EF-hand 3 (171, 172, 175, 176, 179)
D: EF-hand 4 (226)
126:128, 130, 131, 133, 134
96:98, 100, 101, 103:105, 107, 108, 122:124, 126:128, 130, 131, 133, 134, 139, 164, 168, 171, 172, 175, 176, 179, 226
Metals (Me):Ca

Full PDB list

1aj5, 1alv, 1alw, 1df0, 1dvi, 1kfu, 1kfx, 1np8, 1nx0, 1nx1, 1nx2, 1nx3, 1u5i, 3bow, 3df0, 4phj, 4phk, 4phm, 4phn, 4wq2, 4wq3, 5d69 (redundant Pocketome entry)

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1 Me
F
1
0
1
L
1
0
4
F
1
0
5
Q
1
0
7
L
1
0
8
I
1
2
3
L
1
2
4
K
1
2
6
V
1
2
7
V
1
2
8
R
1
3
0
H
1
3
1
L
1
3
4
F
1
3
9
F
1
6
4
W
1
6
8
I
1
7
1
K
1
7
2
Q
1
7
5
A
1
7
6
K
1
7
9
F
2
2
6
[1]1alw.a isa13 . . . . . . . . . . . . . . . . . . . . . . Ca
[1]4phk.a 2ub13 . . . . . . . . . . . . . . . . . . . . . . Ca
[1]4phm.a 2ud16 . . . . . . . . . . . . . . . . . . . . . . Ca
[1]4wq2.a 3su16 . . . . . . . . . . . . . . . . . . . . . . Ca
[1]4wq3.a 3su,3su32 . . . . . . . . . . . . . . . . . . . . . . Ca
[1]5d69.a 57t26 . . . . . . . . . . . . . . . . . . . . . . Ca
[2]1nx0.a DAIDALSSDFTS87 . . . . . . . . . . . . . . . . . . . . . . Ca
[2]1nx1.a DAIDALSSDFT81 . . . . . . . . . . . . . . . . . . . . . . Ca
[2]3bow.b QDPIDALSEDLD92 . . . . . . . . . . . . . . . . . . . G . .
[2]3df0.b HAIDALSSDFT83 . . . . . . . . . . . . . . . . . . . G . .
[3]1kfu.s none . . . . . . . . . . . . . . . . . . . . . .
[4]1u5i.b none . . . . . . . . . . . . . . . . . . . G . .

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
9
6
E
9
7
V
9
8
Q
1
0
0
F
1
0
1
R
1
0
3
L
1
0
4
F
1
0
5
Q
1
0
7
L
1
0
8
N
1
2
2
I
1
2
3
L
1
2
4
K
1
2
6
V
1
2
7
V
1
2
8
R
1
3
0
H
1
3
1
D
1
3
3
L
1
3
4
F
1
3
9
F
1
6
4
W
1
6
8
I
1
7
1
K
1
7
2
Q
1
7
5
A
1
7
6
K
1
7
9
F
2
2
6
[1]1alw.a . . . . . . * . * . . * . * . . * . . . . . . . * . . * . Ca
[1]4phk.a . . . . . . * . . . . * . * . . . . . . . . . . * . . * . Ca
[1]4phm.a . . . . . . * . * . . . . . . . * . . . . . . . . . . * . Ca
[1]4wq2.a . . . . . . * . . . . . . * . . . . . . . . * . . . . . . Ca
[1]4wq3.a . . . . . . * . . . . * . . . . * . . . . . . . . . . . . Ca
[1]5d69.a . . . . . . * . . . . * . . . . * . . . . . . . * . . . . Ca
[2]1nx0.a . . . . . . . . . * . . . . . . * . . . . . * . . . . . . Ca
[2]1nx1.a . . . . . . . . . * . . . . . . * . . . . . * . . . . . . Ca
[2]3bow.b . . E . . K . . . . . . . . . . . . . . . . * . . . G * .
[2]3df0.b . . E . . K . . . . . . . . . . . . . . . . * . . . G . .
[3]1kfu.s . * . * * . . . . . . . . . * * * . * . . . * . . * . . .
[4]1u5i.b . * E . * K . . . . . . . . * * . * . . . . . . . * G . .

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
1alw.a:isa
4phk.a:2ub
4phm.a:2ud
4wq2.a:3su
4wq3.a:3su
5d69.a:57t
1nx0.a:DAIDALSSDFTS
1nx1.a:DAIDALSSDFT
3bow.b:QDPIDALSEDLD
3df0.b:HAIDALSSDFT
1kfu.s is apo
1u5i.b is apo
[1] 1alw.a
0
0 0 0.1 3.2 1.3 5.7 6.2 5.7 7.1 - -
[1] 4phk.a 0.1
0
0.2 0 2.4 0.3 2.8 2.9 2.1 4.4 - -
[1] 4phm.a 0.1 0
0
0 2.5 0.4 4.6 4.6 5.5 4.5 - -
[1] 4wq2.a 0.1 0 0
0.1
1.6 0.2 2.8 3.4 2.7 3.2 - -
[1] 4wq3.a 0 0 0.1 0
0.1
0.2 3.5 4.3 3.3 3.3 - -
[1] 5d69.a 0 0 0.2 0 1.0
0.2
3.3 5.0 3.1 3.7 - -
[2] 1nx0.a 0.5 0.4 1.2 0.5 1.9 0.7
0.1
0.5 0.3 1.1 - -
[2] 1nx1.a 0.5 0.6 1.2 0.4 2.5 0.6 0.1
0.1
0.3 0.9 - -
[2] 3bow.b 0.4 0.3 1.1 0.5 1.6 0.6 1.3 2.1
0
0.7 - -
[2] 3df0.b 0.2 0.2 1.0 0.4 0.7 0.6 0.3 0.4 0.2
0
- -
[3] 1kfu.s 3.7 3.2 2.7 3.0 9.2 4.5 12 12 9.8 9.0
-
-
[4] 1u5i.b 2.9 2.4 2.5 3.0 8.3 3.5 10 9.1 11 9.0 -
-
[Pocket-ligand steric clashes matrix]

Pocket clash dissimilarity (4 clusters)

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
1alw.a
4phk.a
4phm.a
4wq2.a
4wq3.a
5d69.a
1nx0.a
1nx1.a
3bow.b
3df0.b
1kfu.s
1u5i.b
[1] 1alw.a
0
.14 .14 .23 .21 .15 .32 .35 .32 .32 .69 .63
[1] 4phk.a .14
0
.19 .15 .17 .11 .28 .32 .25 .26 .67 .54
[1] 4phm.a .14 .19
0
.17 .15 .17 .29 .32 .30 .31 .64 .58
[1] 4wq2.a .23 .15 .17
0
.13 .14 .19 .23 .19 .18 .59 .51
[1] 4wq3.a .21 .17 .15 .13
0
.08 .20 .22 .23 .20 .57 .56
[1] 5d69.a .15 .11 .17 .14 .08
0
.20 .23 .22 .21 .60 .53
[2] 1nx0.a .32 .28 .29 .19 .20 .20
0
.04 .12 .10 .59 .57
[2] 1nx1.a .35 .32 .32 .23 .22 .23 .04
0
.15 .10 .60 .59
[2] 3bow.b .32 .25 .30 .19 .23 .22 .12 .15
0
.10 .60 .49
[2] 3df0.b .32 .26 .31 .18 .20 .21 .10 .10 .10
0
.60 .52
[3] 1kfu.s .69 .67 .64 .59 .57 .60 .59 .60 .60 .60
0
.32
[4] 1u5i.b .63 .54 .58 .51 .56 .53 .57 .59 .49 .52 .32
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 2.4 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
1alw.a
4phk.a
4phm.a
4wq2.a
4wq3.a
5d69.a
1nx0.a
1nx1.a
3bow.b
3df0.b
1kfu.s
1u5i.b
[1] 1alw.a
0
0.6 0.5 0.6 0.6 0.6 1.2 1.5 1.0 1.5 3.8 3.5
[1] 4phk.a 0.6
0
0.4 0.4 0.3 0.2 1.5 1.9 1.3 1.7 3.7 3.4
[1] 4phm.a 0.5 0.4
0
0.5 0.3 0.4 1.3 1.7 1.2 1.6 3.7 3.4
[1] 4wq2.a 0.6 0.4 0.5
0
0.5 0.3 1.5 1.9 1.4 1.8 3.6 3.4
[1] 4wq3.a 0.6 0.3 0.3 0.5
0
0.4 1.4 1.8 1.3 1.7 3.6 3.4
[1] 5d69.a 0.6 0.2 0.4 0.3 0.4
0
1.5 1.9 1.4 1.8 3.7 3.4
[2] 1nx0.a 1.2 1.5 1.3 1.5 1.4 1.5
0
0.6 0.7 0.8 4.5 4.0
[2] 1nx1.a 1.5 1.9 1.7 1.9 1.8 1.9 0.6
0
0.8 0.8 4.6 4.2
[2] 3bow.b 1.0 1.3 1.2 1.4 1.3 1.4 0.7 0.8
0
0.8 4.2 3.8
[2] 3df0.b 1.5 1.7 1.6 1.8 1.7 1.8 0.8 0.8 0.8
0
4.6 4.1
[3] 1kfu.s 3.8 3.7 3.7 3.6 3.6 3.7 4.5 4.6 4.2 4.6
0
1.1
[4] 1u5i.b 3.5 3.4 3.4 3.4 3.4 3.4 4.0 4.2 3.8 4.1 1.1
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 1.4 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
1alw.a
4phk.a
4phm.a
4wq2.a
4wq3.a
5d69.a
1nx0.a
1nx1.a
3bow.b
3df0.b
1kfu.s
1u5i.b
[1] 1alw.a
0
1.5 1.4 1.7 1.5 1.5 2.2 2.6 2.0 2.4 4.3 4.2
[1] 4phk.a 1.5
0
1.2 1.2 1.3 1.2 2.5 2.8 2.4 2.4 4.0 3.9
[1] 4phm.a 1.4 1.2
0
1.5 1.0 1.0 2.4 2.8 2.2 2.4 4.0 3.9
[1] 4wq2.a 1.7 1.2 1.5
0
1.4 1.4 2.7 3.0 2.4 2.6 4.0 3.9
[1] 4wq3.a 1.5 1.3 1.0 1.4
0
0.8 2.4 2.8 2.3 2.3 4.0 3.9
[1] 5d69.a 1.5 1.2 1.0 1.4 0.8
0
2.5 2.9 2.3 2.3 4.0 4.0
[2] 1nx0.a 2.2 2.5 2.4 2.7 2.4 2.5
0
1.0 1.6 1.6 4.9 4.7
[2] 1nx1.a 2.6 2.8 2.8 3.0 2.8 2.9 1.0
0
1.6 1.7 5.1 4.9
[2] 3bow.b 2.0 2.4 2.2 2.4 2.3 2.3 1.6 1.6
0
1.9 4.6 4.3
[2] 3df0.b 2.4 2.4 2.4 2.6 2.3 2.3 1.6 1.7 1.9
0
4.8 4.8
[3] 1kfu.s 4.3 4.0 4.0 4.0 4.0 4.0 4.9 5.1 4.6 4.8
0
2.1
[4] 1u5i.b 4.2 3.9 3.9 3.9 3.9 4.0 4.7 4.9 4.3 4.8 2.1
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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