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RET1_HUMAN_1_135

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

Composition of the binding site

Protein chains monomer
A1 (RET1_HUMAN):17, 20, 21, 26, 30, 34, 37, 39, 41, 52, 54, 56, 58:61, 63, 77, 78, 107, 109, 118, 12017, 20, 21, 26, 30, 34, 37, 39, 41, 52, 54, 56, 58:61, 63, 77, 78, 107, 109, 118, 120

Full PDB list

1crb, 5h8t, 5h9a, 5ha1, 5hbs, 5ljb, 5ljc, 5ljd, 5lje, 5ljg, 5ljh, 5ljk (redundant Pocketome entry)

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1
F
1
7
Y
2
0
L
2
1
L
3
0
A
3
4
L
3
7
P
3
9
K
4
1
I
5
2
T
5
4
F
5
8
R
5
9
N
6
0
Y
6
1
M
6
3
G
7
7
I
7
8
W
1
0
7
Q
1
0
9
L
1
1
8
M
1
2
0
[1]5ha1.a rne21 . . . . . . . . . . . . . . . . . . . . .
[1]5ljb.a rtl21 . . . . . . . . . . . . . . . . . . . . .
[1]5ljc.a rtl21 . . . . . . . . . . . . . . . . . . L . .
[1]5ljd.a rtl21 . . . . . . . L . . . . . . . . . . . . .
[1]5lje.a rtl21 . . . . . . . L . . . . . . . . . . L . .
[1]5ljg.a plm18 . . . . . . . . . . . . . . . . . . . . .
[1]5ljh.a none . . . . . . . L . . . . . . . . . . . . .
[1]5ljk.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

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PDB.ch
A1
F
1
7
Y
2
0
L
2
1
V
2
6
L
3
0
A
3
4
L
3
7
P
3
9
K
4
1
I
5
2
T
5
4
S
5
6
F
5
8
R
5
9
N
6
0
Y
6
1
M
6
3
G
7
7
I
7
8
W
1
0
7
Q
1
0
9
L
1
1
8
M
1
2
0
[1]5ha1.a . . . . . . . . . . . . . . . . . . . . . . .
[1]5ljb.a . . . . . . . . . . . . . . . . . . . . . . .
[1]5ljc.a . . . . . . . . . . . . . . . . . . . . L . .
[1]5ljd.a . . . . . . . . L . . . . . . . . . . . . . .
[1]5lje.a . . . . . . . . L . . . . . . . . . . . L . .
[1]5ljg.a . . . . . . . . . . . . . . . . . . . . . . .
[1]5ljh.a . . . . . . . . L . . . . . . . . . . . . . .
[1]5ljk.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
5ha1.a:rne
5ljb.a:rtl
5ljc.a:rtl
5ljd.a:rtl
5lje.a:rtl
5ljg.a:plm
5ljh.a is apo
5ljk.a is apo
[1] 5ha1.a
0
0 0.1 0.2 0 0.1 - -
[1] 5ljb.a 0
0
0.1 0.2 0 0.1 - -
[1] 5ljc.a 0 0
0.1
0.1 0 0 - -
[1] 5ljd.a 0 0 0.3
0.1
0.1 0 - -
[1] 5lje.a 0 0 0.3 0
0.1
0 - -
[1] 5ljg.a 0.1 0 0.1 0.2 0
0
- -
[1] 5ljh.a 0 0.1 0.2 0.1 0.1 0
-
-
[1] 5ljk.a 0.1 0 0.1 0.2 0 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
5ha1.a
5ljb.a
5ljc.a
5ljd.a
5lje.a
5ljg.a
5ljh.a
5ljk.a
[1] 5ha1.a
0
0 0 .01 .02 0 .02 0
[1] 5ljb.a 0
0
0 .01 .02 0 .02 0
[1] 5ljc.a 0 0
0
.02 .01 .01 .02 0
[1] 5ljd.a .01 .01 .02
0
0 .02 0 .01
[1] 5lje.a .02 .02 .01 0
0
.02 .01 .02
[1] 5ljg.a 0 0 .01 .02 .02
0
.02 0
[1] 5ljh.a .02 .02 .02 0 .01 .02
0
.02
[1] 5ljk.a 0 0 0 .01 .02 0 .02
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
5ha1.a
5ljb.a
5ljc.a
5ljd.a
5lje.a
5ljg.a
5ljh.a
5ljk.a
[1] 5ha1.a
0
0.4 0.4 0.4 0.4 0.5 0.4 0.5
[1] 5ljb.a 0.4
0
0.1 0.4 0.3 0.2 0.4 0.2
[1] 5ljc.a 0.4 0.1
0
0.4 0.3 0.3 0.3 0.2
[1] 5ljd.a 0.4 0.4 0.4
0
0.2 0.5 0.2 0.5
[1] 5lje.a 0.4 0.3 0.3 0.2
0
0.4 0.2 0.4
[1] 5ljg.a 0.5 0.2 0.3 0.5 0.4
0
0.5 0.2
[1] 5ljh.a 0.4 0.4 0.3 0.2 0.2 0.5
0
0.4
[1] 5ljk.a 0.5 0.2 0.2 0.5 0.4 0.2 0.4
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 0.4 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
5ha1.a
5ljb.a
5ljc.a
5ljd.a
5lje.a
5ljg.a
5ljh.a
5ljk.a
[1] 5ha1.a
0
0.4 0.5 0.6 0.5 0.6 0.7 0.6
[1] 5ljb.a 0.4
0
0.3 0.5 0.4 0.3 0.6 0.3
[1] 5ljc.a 0.5 0.3
0
0.5 0.4 0.4 0.6 0.4
[1] 5ljd.a 0.6 0.5 0.5
0
0.3 0.6 0.5 0.6
[1] 5lje.a 0.5 0.4 0.4 0.3
0
0.5 0.6 0.4
[1] 5ljg.a 0.6 0.3 0.4 0.6 0.5
0
0.6 0.2
[1] 5ljh.a 0.7 0.6 0.6 0.5 0.6 0.6
0
0.6
[1] 5ljk.a 0.6 0.3 0.4 0.6 0.4 0.2 0.6
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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