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APOM_HUMAN_21_188

Apolipoprotein M [Calycin superfamily. Lipocalin family. Highly divergent]

Composition of the binding site

Protein chains monomer
A1 (APOM_HUMAN):39, 40, 43, 47, 62, 63, 69, 71, 73, 82, 84, 98, 100, 102, 111, 116, 123, 132, 134, 136, 143, 145, 14739, 40, 43, 47, 62, 63, 69, 71, 73, 82, 84, 98, 100, 102, 111, 116, 123, 132, 134, 136, 143, 145, 147

Full PDB list

2wew, 2wex, 2yg2

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1
F
3
9
P
4
0
H
4
3
W
4
7
T
6
2
F
6
3
I
6
9
F
7
1
M
7
3
L
8
2
L
8
4
R
9
8
W
1
0
0
Y
1
0
2
L
1
1
1
R
1
1
6
L
1
2
3
I
1
3
2
L
1
3
4
E
1
3
6
R
1
4
3
L
1
4
5
Y
1
4
7
[1]2wew.a myr16 . . . . . . . . . . . . . . . . . . . . . . .
[1]2wex.a gym21 . . . . . . . . . . . . . . . - . . . . . . .
[1]2yg2.b s1p25 . . . . . . . . . . . . . . . . . . . . . . .

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
F
3
9
P
4
0
H
4
3
W
4
7
T
6
2
F
6
3
I
6
9
F
7
1
M
7
3
L
8
2
L
8
4
R
9
8
W
1
0
0
Y
1
0
2
L
1
1
1
R
1
1
6
L
1
2
3
I
1
3
2
L
1
3
4
E
1
3
6
R
1
4
3
L
1
4
5
Y
1
4
7
[1]2wew.a . . . . . . . . . . . * . . . . . . . . . . .
[1]2wex.a . . . . . . . . . . . . . . * - . . . . . . .
[1]2yg2.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
2wew.a:myr
2wex.a:gym
2yg2.b:s1p
[1] 2wew.a
0
0.3 1.8
[1] 2wex.a 0
0.1
1.5
[1] 2yg2.b 0.8 0.7
0
[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
2wew.a
2wex.a
2yg2.b
[1] 2wew.a
0
.08 .13
[1] 2wex.a .08
0
.10
[1] 2yg2.b .13 .10
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

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
2wew.a
2wex.a
2yg2.b
[1] 2wew.a
0
0.2 1.0
[1] 2wex.a 0.2
0
0.9
[1] 2yg2.b 1.0 0.9
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 0.2 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
2wew.a
2wex.a
2yg2.b
[1] 2wew.a
0
0.7 2.0
[1] 2wex.a 0.7
0
1.3
[1] 2yg2.b 2.0 1.3
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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