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CLPP_STAA8_1_195

ATP-dependent Clp protease proteolytic subunit [Peptidase S14 family]

Composition of the binding site

Protein chains monomer
A1 (CLPP_STAA8):71, 98, 99, 101, 102, 122:128, 132, 138:143, 146, 147, 150, 151, 154, 16971, 98, 99, 101, 102, 122:128, 132, 138:143, 146, 147, 150, 151, 154, 169

Full PDB list

3qwd, 3st9, 3sta, 3v5e, 4emm, 4emp, 4mxi, 5c90, 5dl1, 5vz2, 5w18 (redundant Pocketome entry)

Pocket contact map

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PDB.ch
   
ligand
A1
V
7
1
S
9
8
S
1
0
1
I
1
2
2
H
1
2
3
Q
1
2
4
P
1
2
5
L
1
2
6
Q
1
3
2
H
1
4
2
I
1
4
3
T
1
4
6
R
1
4
7
L
1
5
0
N
1
5
1
L
1
5
4
T
1
6
9
[1]4emp.v none . . . . . . . . . . . . . . . . .
[1]5dl1.a 5c226 . . . . . . . . . . . . . . . . .
[2]3qwd.d none . . . . . . . . . . . . . . . . .
[2]4mxi.c 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
V
7
1
S
9
8
M
9
9
S
1
0
1
F
1
0
2
I
1
2
2
H
1
2
3
Q
1
2
4
P
1
2
5
L
1
2
6
G
1
2
7
G
1
2
8
Q
1
3
2
I
1
3
8
A
1
3
9
A
1
4
0
N
1
4
1
H
1
4
2
I
1
4
3
T
1
4
6
R
1
4
7
L
1
5
0
N
1
5
1
L
1
5
4
T
1
6
9
[1]4emp.v . . . . . . . . * . . . . . . . . . . . . . . . .
[1]5dl1.a . . . . . . . . . . . . . . . . . . . . . . . . .
[2]3qwd.d . . . . . . . * . . . . . . . . * * . . * . . . .
[2]4mxi.c . * . . . . . * . . - - - . . . . * . . * . . . .

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
4emp.v is apo
5dl1.a:5c2
3qwd.d is apo
4mxi.c is apo
[1] 4emp.v
-
5.5 - -
[1] 5dl1.a -
0.2
- -
[2] 3qwd.d - 11
-
-
[2] 4mxi.c - 6.2 -
-
[Pocket-ligand steric clashes matrix]

Pocket clash dissimilarity (2 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
4emp.v
5dl1.a
3qwd.d
4mxi.c
[1] 4emp.v
0
.19 .50 .33
[1] 5dl1.a .19
0
.39 .22
[2] 3qwd.d .50 .39
0
.19
[2] 4mxi.c .33 .22 .19
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 4.7 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
4emp.v
5dl1.a
3qwd.d
4mxi.c
[1] 4emp.v
0
2.9 6.8 4.8
[1] 5dl1.a 2.9
0
6.3 5.0
[2] 3qwd.d 6.8 6.3
0
2.1
[2] 4mxi.c 4.8 5.0 2.1
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 3.9 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
4emp.v
5dl1.a
3qwd.d
4mxi.c
[1] 4emp.v
0
4.0 7.9 5.5
[1] 5dl1.a 4.0
0
7.5 6.3
[2] 3qwd.d 7.9 7.5
0
2.1
[2] 4mxi.c 5.5 6.3 2.1
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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