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CASP7_HUMAN_52_303_allosteric

Caspase-7 [Peptidase C14A family]

Composition of the binding site

Protein chains monomer
A1 (CASP7_HUMAN):147, 148, 159, 160, 183, 187, 206:215, 221, 223, 225:227, 290, 292, 294147, 148, 159, 160, 183, 187, 206:215, 221, 223, 225:227, 290, 292, 294

Full PDB list

1f1j, 1gqf, 1i4o, 1i51, 1k86, 1k88, 1kmc, 1shj, 1shl, 2ql5, 2ql7, 2ql9, 2qlb, 2qlf, 2qlj, 3edr, 3h1p, 3ibc, 3ibf, 3r5k, 4fdl, 4hq0, 4hqr, 4jb8, 4jj8, 4jr1, 4jr2, 4lsz, 4zvo, 4zvp, 4zvq, 4zvr, 4zvs, 4zvt, 4zvu, 5ic6, 5k20, 5v6u, 5v6z (redundant Pocketome entry)

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1
I
1
5
9
K
1
6
0
I
1
8
3
Y
2
1
1
I
2
1
3
P
2
1
4
V
2
1
5
F
2
2
1
Y
2
2
3
C
2
9
0
V
2
9
2
[1]1shj.b nxn,nxn32 . . . . . . . . . * .
[1]1shl.b fxn,fxn32 . . . - . . . . . * .
[2]3h1p.a none . . . . A . . . . . .
[2]3r5k.a none . . . . . . . . . . .
[3]1k88.b none . . . . . . . . . . .

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
E
1
4
7
N
1
4
8
I
1
5
9
K
1
6
0
I
1
8
3
R
1
8
7
D
2
0
6
A
2
0
7
N
2
0
8
P
2
0
9
R
2
1
0
Y
2
1
1
K
2
1
2
I
2
1
3
P
2
1
4
V
2
1
5
F
2
2
1
Y
2
2
3
T
2
2
5
V
2
2
6
P
2
2
7
C
2
9
0
V
2
9
2
M
2
9
4
[1]1shj.b . . . . . . - - - . . . . * . . . . . . . * . .
[1]1shl.b . . . . . . - - - - - - - . . . . . . . . * . .
[2]3h1p.a . . . . . * - - - - - . . A . . . * . . . * . .
[2]3r5k.a . . . . . * - - - - C . . . . . . * . . . * . .
[3]1k88.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
1shj.b:nxn
1shl.b:fxn
3h1p.a is apo
3r5k.a is apo
1k88.b is apo
[1] 1shj.b
0.4
3.2 - - -
[1] 1shl.b 0.4
0.6
- - -
[2] 3h1p.a 5.5 4.4
-
- -
[2] 3r5k.a 5.7 4.2 -
-
-
[3] 1k88.b 4.6 11 - -
-
[Pocket-ligand steric clashes matrix]

Pocket clash dissimilarity (3 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
1shj.b
1shl.b
3h1p.a
3r5k.a
1k88.b
[1] 1shj.b
0
.11 .33 .34 .42
[1] 1shl.b .11
0
.25 .26 .45
[2] 3h1p.a .33 .25
0
.01 .66
[2] 3r5k.a .34 .26 .01
0
.66
[3] 1k88.b .42 .45 .66 .66
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 5.4 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
1shj.b
1shl.b
3h1p.a
3r5k.a
1k88.b
[1] 1shj.b
0
0.9 11 14 3.7
[1] 1shl.b 0.9
0
6.8 6.8 1.0
[2] 3h1p.a 11 6.8
0
0.7 9.6
[2] 3r5k.a 14 6.8 0.7
0
12
[3] 1k88.b 3.7 1.0 9.6 12
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 3.7 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
1shj.b
1shl.b
3h1p.a
3r5k.a
1k88.b
[1] 1shj.b
0
2.4 11 13 5.4
[1] 1shl.b 2.4
0
7.1 7.6 2.5
[2] 3h1p.a 11 7.1
0
1.4 10
[2] 3r5k.a 13 7.6 1.4
0
12
[3] 1k88.b 5.4 2.5 10 12
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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