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CBX7_HUMAN_6_65

Chromobox protein homolog 7

Composition of the binding site

Protein chains monomer [domain annotation]
A1 (CBX7_HUMAN):D: Chromo (11:13, 20, 22, 29, 32, 33, 35, 38:43, 46:53)
3:10
3:13, 20, 22, 29, 32, 33, 35, 38:43, 46:53
Metals (Me):Mg/Ni/Zn

Full PDB list

4mn3, 4x3k, 4x3s, 4x3t, 4x3u, 5epj (Pocketome entry); 5ejw (unprocessed)

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1 Me
A
5
I
6
G
7
E
8
Q
9
V
1
0
F
1
1
A
1
2
V
1
3
R
2
0
R
2
2
L
2
9
W
3
2
W
3
5
Y
3
9
S
4
0
T
4
1
W
4
2
E
4
3
E
4
6
H
4
7
I
4
8
L
4
9
D
5
0
P
5
1
R
5
2
L
5
3
[1]4mn3.a aceFAYm3lSnh250 - - . . . . . . . . . . . . . . . . . . . . . . . . . Mg
[1]4x3s.a fe,RGFALm3lSTH75 - M . . . . . . . . . . . . . . . . . . . . . . . . .
[1]4x3s.b RGFALm3lSTH74 - M . . . . . . . . . . . . . . . . . . . . . . . . .
[1]5epj.a 5r0FALely.5r557 - - - - . . . . . . . . . . . . . . . . . . . . . . .
[2]4x3t.b 45e,45e58 H M . . . . . . . . . . . . . . . . . . . . . . . . . Zn
[2]4x3t.d 45e,45e,zn59 H M . . . . . . . . . . . . . . . . . . . . . . . . .
[2]4x3u.b svr86 - - - - - . . . . . . . . . . . . . . . . . . . . . .
[3]4x3k.a KAARm3lSA53 H M . . . . . . . . . . . . . . . . . . . . . . . . . Ni

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
3
S
4
A
5
I
6
G
7
E
8
Q
9
V
1
0
F
1
1
A
1
2
V
1
3
R
2
0
R
2
2
L
2
9
W
3
2
K
3
3
W
3
5
K
3
8
Y
3
9
S
4
0
T
4
1
W
4
2
E
4
3
E
4
6
H
4
7
I
4
8
L
4
9
D
5
0
P
5
1
R
5
2
L
5
3
[1]4mn3.a - - - - . . * * . . . . . . . . * . . . . . . . . . . . . . . Mg
[1]4x3s.a - - - M . * * * . . . . . . . . * . . . . . . . . . . . . . .
[1]4x3s.b - - - M . * * * . . . . . . . . * . . . . . . . . . . . . . .
[1]5epj.a - - - - - - * * * . . . . . . . . . . . . . . . . . . . . . .
[2]4x3t.b - - H M . . . . * . . . . . . . . . . . . . . . . . . . . . . Zn
[2]4x3t.d - - H M . . . . . . . . . . . . . . . . . . . . . . . . . . .
[2]4x3u.b - - - - - - - . . . . . . . . . * . . . . . . . * . . . . . .
[3]4x3k.a G * H M . * * * . . . . . . . . * . . . . . . . . . . . . . . Ni

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
4mn3.a:aceFAYm3lSnh2
4x3s.a:RGFALm3lSTH,fe
4x3s.b:RGFALm3lSTH
5epj.a:5r0FALely.5r5
4x3t.b:45e
4x3t.d:45e,zn
4x3u.b:svr
4x3k.a:KAARm3lSA
[1] 4mn3.a
0
0.6 0.6 0.8 1.4 6.9 3.8 0.8
[1] 4x3s.a 0.6
0
0.1 1.0 1.0 8.3 5.7 0.3
[1] 4x3s.b 0.5 0
0
1.0 1.0 8.4 5.7 0.3
[1] 5epj.a 0.4 0.2 0.2
0
0.8 6.5 3.3 0.3
[2] 4x3t.b 1.1 2.2 2.2 2.0
0
0.6 0.3 2.3
[2] 4x3t.d 0.6 0.7 0.7 0.9 0.1
0.1
0.4 1.1
[2] 4x3u.b 0.4 0.9 0.9 2.1 2.4 3.9
0.1
1.1
[3] 4x3k.a 1.8 0.2 0.6 1.4 0.9 12 8.0
0
[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
4mn3.a
4x3s.a
4x3s.b
5epj.a
4x3t.b
4x3t.d
4x3u.b
4x3k.a
[1] 4mn3.a
0
.12 .12 .10 .33 .30 .31 .28
[1] 4x3s.a .12
0
.01 .17 .37 .35 .39 .27
[1] 4x3s.b .12 .01
0
.16 .37 .35 .38 .27
[1] 5epj.a .10 .17 .16
0
.29 .23 .35 .32
[2] 4x3t.b .33 .37 .37 .29
0
.08 .19 .51
[2] 4x3t.d .30 .35 .35 .23 .08
0
.19 .48
[2] 4x3u.b .31 .39 .38 .35 .19 .19
0
.47
[3] 4x3k.a .28 .27 .27 .32 .51 .48 .47
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 2.0 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
4mn3.a
4x3s.a
4x3s.b
5epj.a
4x3t.b
4x3t.d
4x3u.b
4x3k.a
[1] 4mn3.a
0
1.0 1.0 0.8 4.0 5.9 1.6 1.5
[1] 4x3s.a 1.0
0
0.1 0.6 4.9 7.2 1.5 2.5
[1] 4x3s.b 1.0 0.1
0
0.6 4.8 7.2 1.5 2.5
[1] 5epj.a 0.8 0.6 0.6
0
2.3 4.4 1.4 0.6
[2] 4x3t.b 4.0 4.9 4.8 2.3
0
5.7 0.8 5.5
[2] 4x3t.d 5.9 7.2 7.2 4.4 5.7
0
4.1 7.3
[2] 4x3u.b 1.6 1.5 1.5 1.4 0.8 4.1
0
1.5
[3] 4x3k.a 1.5 2.5 2.5 0.6 5.5 7.3 1.5
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 1.5 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
4mn3.a
4x3s.a
4x3s.b
5epj.a
4x3t.b
4x3t.d
4x3u.b
4x3k.a
[1] 4mn3.a
0
1.4 1.3 1.3 4.3 6.3 2.1 1.6
[1] 4x3s.a 1.4
0
0.5 1.1 4.7 6.8 1.9 2.1
[1] 4x3s.b 1.3 0.5
0
1.1 4.7 6.8 1.9 2.1
[1] 5epj.a 1.3 1.1 1.1
0
2.3 4.6 2.1 0.9
[2] 4x3t.b 4.3 4.7 4.7 2.3
0
6.0 1.5 5.7
[2] 4x3t.d 6.3 6.8 6.8 4.6 6.0
0
4.4 7.9
[2] 4x3u.b 2.1 1.9 1.9 2.1 1.5 4.4
0
1.9
[3] 4x3k.a 1.6 2.1 2.1 0.9 5.7 7.9 1.9
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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