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COMP_HUMAN_28_72

Cartilage oligomeric matrix protein [Thrombospondin family]

Composition of the binding site

Protein chains homopentamer [domain annotation]
A1 (COMP_HUMAN):R: COMP N-terminal (59, 62, 66, 69, 71, 72)59, 62, 66, 69, 71, 72
A2 (COMP_HUMAN):R: COMP N-terminal (59, 62, 66, 69, 71, 72)59, 62, 66, 69, 71, 72
A3 (COMP_HUMAN):R: COMP N-terminal (59, 62, 66, 69, 71, 72)59, 62, 66, 69, 71, 72
A4 (COMP_HUMAN):R: COMP N-terminal (59, 62, 66, 69, 71, 72)59, 62, 66, 69, 71, 72
A5 (COMP_HUMAN):R: COMP N-terminal (59, 62, 66, 69, 71, 72)59, 62, 66, 69, 71, 72
Cofactors (cF):myr/ste

Full PDB list

1fbm, 1mz9, 1vdf, 3v2n, 3v2p, 3v2q, 3v2r (redundant Pocketome entry)

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1 A2 A3 A4 A5 cF
I
5
9
L
6
2
V
6
6
A
7
1
C
7
2
I
5
9
L
6
2
V
6
6
C
6
9
A
7
1
C
7
2
I
5
9
L
6
2
V
6
6
C
6
9
A
7
1
C
7
2
I
5
9
L
6
2
V
6
6
C
6
9
A
7
1
I
5
9
L
6
2
V
6
6
C
6
9
A
7
1
C
7
2
[1]1mz9.a vdy29 . . . . . . . . . . . . . . . . . . . . - - . . . . . .
[1]1mz9.b vdy29 . . . . . . . . . . . . . . . . . . . . . . . . . - - -
[1]1mz9.c vdy29 . . . . . . . . . . . . . . - - - . . . . . . . . . . .
[1]1mz9.d vdy29 . . . - - . . . . . . . . . . . . . . . . . . . . . . .
[1]3v2n.a none . . . . . . . . . . . . . . . . . . . . . . . . . . . . myr
[1]3v2p.a none . . . . . . . . . . . . . . . . . . . . . . . . . . . . ste
[1]3v2p.b none . . . . . . . . . . . . . . . . . . . . . . . . . . . . ste
[1]3v2p.c none . . . . . . . . . . . . . . . . . . . . . . . . . . . . ste
[1]3v2p.d none . . . . . . . . . . . . . . . . . . . . . . . . . . . . ste

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 A2 A3 A4 A5 cF
I
5
9
L
6
2
V
6
6
C
6
9
A
7
1
C
7
2
I
5
9
L
6
2
V
6
6
C
6
9
A
7
1
C
7
2
I
5
9
L
6
2
V
6
6
C
6
9
A
7
1
C
7
2
I
5
9
L
6
2
V
6
6
C
6
9
A
7
1
C
7
2
I
5
9
L
6
2
V
6
6
C
6
9
A
7
1
C
7
2
[1]1mz9.a . . . . . . . . . . . . . . . . . . . . . - - - . . . . . .
[1]1mz9.b . . . . . . . . . . . . . . . . . . . . . . . . . . . - - -
[1]1mz9.c . . . . . . . . . . . . . . . - - - . . . . . . . . . . . .
[1]1mz9.d . . . - - - . . . . . . . . . . . . . . . . . . . . . . . .
[1]3v2n.a . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . myr
[1]3v2p.a . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ste
[1]3v2p.b . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ste
[1]3v2p.c . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ste
[1]3v2p.d . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ste

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
1mz9.a:vdy
1mz9.b:vdy
1mz9.c:vdy
1mz9.d:vdy
3v2n.a is apo
3v2p.a is apo
3v2p.b is apo
3v2p.c is apo
3v2p.d is apo
[1] 1mz9.a
0
0.7 0.6 0.7 - - - - -
[1] 1mz9.b 0.5
0
1.1 1.3 - - - - -
[1] 1mz9.c 0.7 1.2
0
0.9 - - - - -
[1] 1mz9.d 0.7 0.9 1.0
0
- - - - -
[1] 3v2n.a 1.2 1.3 1.5 1.6
-
- - - -
[1] 3v2p.a 1.2 1.1 1.7 1.6 -
-
- - -
[1] 3v2p.b 1.3 1.1 1.5 1.5 - -
-
- -
[1] 3v2p.c 1.6 1.7 1.2 1.3 - - -
-
-
[1] 3v2p.d 1.2 1.8 2.1 1.4 - - - -
-
[Pocket-ligand steric clashes matrix]

Pocket clash dissimilarity (1 cluster)

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
1mz9.a
1mz9.b
1mz9.c
1mz9.d
3v2n.a
3v2p.a
3v2p.b
3v2p.c
3v2p.d
[1] 1mz9.a
0
.05 .05 .06 .05 .06 .07 .08 .09
[1] 1mz9.b .05
0
.08 .07 .08 .07 .04 .09 .11
[1] 1mz9.c .05 .08
0
.09 .07 .07 .07 .06 .12
[1] 1mz9.d .06 .07 .09
0
.08 .10 .07 .09 .06
[1] 3v2n.a .05 .08 .07 .08
0
.03 .09 .06 .08
[1] 3v2p.a .06 .07 .07 .10 .03
0
.07 .05 .10
[1] 3v2p.b .07 .04 .07 .07 .09 .07
0
.06 .10
[1] 3v2p.c .08 .09 .06 .09 .06 .05 .06
0
.11
[1] 3v2p.d .09 .11 .12 .06 .08 .10 .10 .11
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 0.7 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
1mz9.a
1mz9.b
1mz9.c
1mz9.d
3v2n.a
3v2p.a
3v2p.b
3v2p.c
3v2p.d
[1] 1mz9.a
0
0.7 0.6 0.9 0.4 0.3 0.8 0.6 1.2
[1] 1mz9.b 0.7
0
0.8 0.7 0.8 0.7 0.3 0.8 0.9
[1] 1mz9.c 0.6 0.8
0
1.0 0.7 0.7 0.8 0.3 1.2
[1] 1mz9.d 0.9 0.7 1.0
0
0.9 0.9 0.8 0.9 0.4
[1] 3v2n.a 0.4 0.8 0.7 0.9
0
0.3 0.8 0.7 1.1
[1] 3v2p.a 0.3 0.7 0.7 0.9 0.3
0
0.8 0.7 1.1
[1] 3v2p.b 0.8 0.3 0.8 0.8 0.8 0.8
0
0.8 1.0
[1] 3v2p.c 0.6 0.8 0.3 0.9 0.7 0.7 0.8
0
1.2
[1] 3v2p.d 1.2 0.9 1.2 0.4 1.1 1.1 1.0 1.2
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 0.7 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
1mz9.a
1mz9.b
1mz9.c
1mz9.d
3v2n.a
3v2p.a
3v2p.b
3v2p.c
3v2p.d
[1] 1mz9.a
0
0.7 0.6 0.9 0.4 0.3 0.8 0.6 1.1
[1] 1mz9.b 0.7
0
0.8 0.8 0.7 0.7 0.4 0.8 0.9
[1] 1mz9.c 0.6 0.8
0
0.9 0.7 0.7 0.7 0.4 1.1
[1] 1mz9.d 0.9 0.8 0.9
0
0.9 0.9 0.8 0.9 0.4
[1] 3v2n.a 0.4 0.7 0.7 0.9
0
0.3 0.8 0.7 1.1
[1] 3v2p.a 0.3 0.7 0.7 0.9 0.3
0
0.7 0.6 1.1
[1] 3v2p.b 0.8 0.4 0.7 0.8 0.8 0.7
0
0.7 1.0
[1] 3v2p.c 0.6 0.8 0.4 0.9 0.7 0.6 0.7
0
1.1
[1] 3v2p.d 1.1 0.9 1.1 0.4 1.1 1.1 1.0 1.1
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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