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RABP1_MOUSE_2_137

Cellular retinoic acid-binding protein 1 [Calycin superfamily. Fatty-acid binding protein (FABP) family]

Composition of the binding site

Protein chains monomer [domain annotation]
A1 (RABP1_MOUSE):R: Retinoic acid binding (132, 134)
16, 20, 25, 29, 32, 33, 36, 37, 40, 55, 57, 59, 60, 77:79, 121, 123
16, 20, 25, 29, 32, 33, 36, 37, 40, 55, 57, 59, 60, 77:79, 121, 123, 132, 134

Full PDB list

1cbi, 1cbr, 2cbr

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1
F
1
6
L
2
0
V
2
5
L
2
9
V
3
2
A
3
3
A
3
7
P
4
0
T
5
5
T
5
7
V
5
9
R
6
0
V
7
7
D
7
8
G
7
9
L
1
2
1
F
1
2
3
R
1
3
2
Y
1
3
4
[1]1cbi.b none . . . . . . . . . . . . . . . . . . .
[1]1cbr.a rea22 . . . . . . . . . . . . . . . . . . .
[1]2cbr.a a8026 . . . . . . . . . . . . . . . . . . .

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
1
6
L
2
0
V
2
5
L
2
9
V
3
2
A
3
3
A
3
6
A
3
7
P
4
0
T
5
5
T
5
7
V
5
9
R
6
0
V
7
7
D
7
8
G
7
9
L
1
2
1
F
1
2
3
R
1
3
2
Y
1
3
4
[1]1cbi.b . . . . . . . . . . . . . . . . . . . .
[1]1cbr.a . . . . . . . . . . . . . . . . . . . .
[1]2cbr.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
1cbi.b is apo
1cbr.a:rea
2cbr.a:a80
[1] 1cbi.b
-
0.5 0.5
[1] 1cbr.a -
0.1
0.4
[1] 2cbr.a - 0.1
0.1
[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
1cbi.b
1cbr.a
2cbr.a
[1] 1cbi.b
0
.04 .02
[1] 1cbr.a .04
0
.02
[1] 2cbr.a .02 .02
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 0.6 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
1cbi.b
1cbr.a
2cbr.a
[1] 1cbi.b
0
1.1 1.0
[1] 1cbr.a 1.1
0
0.5
[1] 2cbr.a 1.0 0.5
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
1cbi.b
1cbr.a
2cbr.a
[1] 1cbi.b
0
1.3 1.2
[1] 1cbr.a 1.3
0
0.6
[1] 2cbr.a 1.2 0.6
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

L C X E | Background Color: | Anaglyph Stereo:

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