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CSN5_HUMAN_10_250

COP9 signalosome complex subunit 5 [Peptidase M67A family. CSN5 subfamily]

Composition of the binding site

Protein chains monomer [domain annotation]
A1 (CSN5_HUMAN):D: MPN (75:78, 99:107, 111:115, 117, 136, 138, 140, 143, 150, 151, 154, 157, 158)75:78, 99:107, 111:115, 117, 136, 138, 140, 143, 150, 151, 154, 157, 158
Metals (Me):Zn

Full PDB list

4f7o, 5jog, 5joh, 5m5q

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1 Me
E
7
6
V
7
7
M
7
8
P
9
9
W
1
3
6
H
1
3
8
H
1
4
0
Y
1
4
3
I
1
5
0
D
1
5
1
T
1
5
4
L
1
5
7
N
1
5
8
[1]5jog.a 6lt37 . . . . . . . . . . . . . Zn
[1]5joh.a 6m326 . . . . . . . . . . . . . Zn
[1]5m5q.a 7k141 . . . . . . . . . . . . . Zn
[2]4f7o.b none . . * . . . . . . . . . . Zn

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
L
7
5
E
7
6
V
7
7
M
7
8
P
9
9
V
1
0
0
E
1
0
1
G
1
0
2
T
1
0
3
E
1
0
4
T
1
0
5
R
1
0
6
V
1
0
7
A
1
1
1
A
1
1
2
A
1
1
3
Y
1
1
4
E
1
1
5
M
1
1
7
W
1
3
6
H
1
3
8
H
1
4
0
Y
1
4
3
I
1
5
0
D
1
5
1
T
1
5
4
L
1
5
7
N
1
5
8
[1]5jog.a . . . . . - - - - - - - . . . . . . . . . . . . . . . . Zn
[1]5joh.a . . . . . - - - - - - - . . . . . . . . . . . . . . . . Zn
[1]5m5q.a . . . . . - - - - - - - - . . . . . . . . . . . . . . . Zn
[2]4f7o.b . * . * . * * * * . . * . . . * * . mse . . . . . . . . . Zn

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
5jog.a:6lt
5joh.a:6m3
5m5q.a:7k1
4f7o.b is apo
[1] 5jog.a
0
0 0 -
[1] 5joh.a 0
0
0 -
[1] 5m5q.a 0.1 0.1
0
-
[2] 4f7o.b 12 6.5 14
-
[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
5jog.a
5joh.a
5m5q.a
4f7o.b
[1] 5jog.a
0
0 0 .69
[1] 5joh.a 0
0
0 .69
[1] 5m5q.a 0 0
0
.69
[2] 4f7o.b .69 .69 .69
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 0.8 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
5jog.a
5joh.a
5m5q.a
4f7o.b
[1] 5jog.a
0
0.2 0.5 8.5
[1] 5joh.a 0.2
0
0.5 8.4
[1] 5m5q.a 0.5 0.5
0
7.4
[2] 4f7o.b 8.5 8.4 7.4
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 0.5 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
5jog.a
5joh.a
5m5q.a
4f7o.b
[1] 5jog.a
0
0.4 0.8 7.8
[1] 5joh.a 0.4
0
0.8 7.8
[1] 5m5q.a 0.8 0.8
0
6.9
[2] 4f7o.b 7.8 7.8 6.9
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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