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APOD_HUMAN_23_189

Apolipoprotein D [Calycin superfamily. Lipocalin family]

Composition of the binding site

Protein chains monomer
A1 (APOD_HUMAN):48, 54, 64, 66, 78, 109, 118, 147, 14948, 54, 64, 66, 78, 109, 118, 147, 149

Full PDB list

2hzq, 2hzr

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1
E
4
8
T
5
4
A
6
4
Y
6
6
N
7
8
F
1
0
9
Y
1
1
8
W
1
4
7
L
1
4
9
[1]2hzq.a str23 . . . . . . . . .
[1]2hzr.a 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

[download in TSV format]
   
PDB.ch
A1
E
4
8
T
5
4
A
6
4
Y
6
6
N
7
8
F
1
0
9
Y
1
1
8
W
1
4
7
L
1
4
9
[1]2hzq.a . . . . . . . . .
[1]2hzr.a . . . . . . . . .

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
2hzq.a:str
2hzr.a is apo
[1] 2hzq.a
0
-
[1] 2hzr.a 0.4
-
[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
2hzq.a
2hzr.a
[1] 2hzq.a
0
.04
[1] 2hzr.a .04
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 0.5 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
2hzq.a
2hzr.a
[1] 2hzq.a
0
0.4
[1] 2hzr.a 0.4
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
2hzq.a
2hzr.a
[1] 2hzq.a
0
0.9
[1] 2hzr.a 0.9
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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