If you see this message after the page is completely loaded, then JavaScript is not supported or disabled in your browser. Please consider enabling JavaScript for this site.

RARG_HUMAN_178_421

Retinoic acid receptor gamma [Nuclear hormone receptor family. NR1 subfamily]

Composition of the binding site

Protein chains monomer [domain annotation]
A1 (RARG_HUMAN):R: Hinge (201)
R: Ligand-binding (227, 230, 233, 234, 237, 268, 271, 272, 274, 275, 278, 288, 289, 303, 304, 307, 393, 396, 397, 400, 408, 412, 415, 416)
201, 227, 230, 233, 234, 237, 268, 271, 272, 274, 275, 278, 288, 289, 303, 304, 307, 393, 396, 397, 400, 408, 412, 415, 416
Cofactors (cF):lmu

Full PDB list

1exa, 1exx, 1fcx, 1fcy, 1fcz, 1fd0, 2lbd, 3lbd, 4lbd, 5m24 (redundant Pocketome entry)

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1 cF
F
2
0
1
W
2
2
7
F
2
3
0
L
2
3
3
A
2
3
4
C
2
3
7
L
2
6
8
L
2
7
1
M
2
7
2
R
2
7
4
I
2
7
5
R
2
7
8
F
2
8
8
S
2
8
9
G
3
0
3
F
3
0
4
L
3
0
7
G
3
9
3
R
3
9
6
A
3
9
7
L
4
0
0
M
4
0
8
I
4
1
2
M
4
1
5
L
4
1
6
[1]1exa.a 39429 . . . . . . . . . . . . . . . . . . . . . . . . . lmu
[1]1exx.a 96129 . . . . . . . . . . . . . . . . . . . . . . . . . lmu
[1]1fcx.a 18429 . . . . . . . . . . . . . . . . . . . . . . . . . lmu
[1]1fcy.a 56429 . . . . . . . . . . . . . . . . . . . . . . . . . lmu
[1]1fcz.a 15627 . . . . . . . . . . . . . . . . . . . . . . . . . lmu
[1]1fd0.a 25430 . . . . . . . . . . . . . . . . . . . . . . . . . lmu
[1]2lbd.a rea22 . . . . . . . . . . . . . . . . . . . . . . . . .
[1]5m24.a 9cr22 . . . . . . . . . . . . . . . . . . . . . . . . . lmu

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 cF
F
2
0
1
W
2
2
7
F
2
3
0
L
2
3
3
A
2
3
4
C
2
3
7
L
2
6
8
L
2
7
1
M
2
7
2
R
2
7
4
I
2
7
5
R
2
7
8
F
2
8
8
S
2
8
9
G
3
0
3
F
3
0
4
L
3
0
7
G
3
9
3
R
3
9
6
A
3
9
7
L
4
0
0
M
4
0
8
I
4
1
2
M
4
1
5
L
4
1
6
[1]1exa.a . . . . . . . . . . . . . . . . . . . . . . . . . lmu
[1]1exx.a . . . . . . . . . . . . . . . . . . . . . . . . . lmu
[1]1fcx.a . . . . . . . . . . . . . . . . . . . . . . . . . lmu
[1]1fcy.a . . . . . . . . . . . . . . . . . . . . . . . . . lmu
[1]1fcz.a . . . . . . . . . . . . . . . . . . . . . . . . . lmu
[1]1fd0.a . . . . . . . . . . . . . . . . . . . . . . . . . lmu
[1]2lbd.a . . . . . . . . . . . . . . . . . . . . . . . . .
[1]5m24.a . . . . . . . . . . . . . . . . . . . . . . . . . lmu

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

zoom: [−] [+]; [view as image]; [download as text]

pocketligand
≥10
9
8
7
6
5
4
3
2
1
0
1exa.a:394
1exx.a:961
1fcx.a:184
1fcy.a:564
1fcz.a:156
1fd0.a:254
2lbd.a:rea
5m24.a:9cr
[1] 1exa.a
0.1
0.1 0.3 0.3 0 0.2 0 0.1
[1] 1exx.a 0.1
0.2
0.3 0.3 0.1 0.3 0.1 0.3
[1] 1fcx.a 0 0.2
0.1
0.1 0.1 0.1 0 0.1
[1] 1fcy.a 0.1 0.2 0
0.1
0 0 0 0.1
[1] 1fcz.a 0.2 0.2 0.3 0.3
0.1
0.3 0.1 0.1
[1] 1fd0.a 0 0.3 0.1 0.1 0
0.1
0 0.1
[1] 2lbd.a 0.1 0.4 0.1 0.1 0.1 0.2
0
0.1
[1] 5m24.a 0.2 0.4 0.5 0.7 0.3 0.4 0.1
0
[Pocket-ligand steric clashes matrix]

Pocket clash dissimilarity (1 cluster)

Pockets (x) vs pockets (y) colored by ligand clash profile difference

zoom: [−] [+]; [view as image]; [download as text]

pocketpocket
≥1.
.9
.8
.7
.6
.5
.4
.3
.2
.1
.0
1exa.a
1exx.a
1fcx.a
1fcy.a
1fcz.a
1fd0.a
2lbd.a
5m24.a
[1] 1exa.a
0
.01 .01 .01 0 .02 .02 .04
[1] 1exx.a .01
0
.02 .02 .01 .02 .03 .05
[1] 1fcx.a .01 .02
0
0 .01 0 .01 .04
[1] 1fcy.a .01 .02 0
0
.01 0 .01 .04
[1] 1fcz.a 0 .01 .01 .01
0
.02 .02 .04
[1] 1fd0.a .02 .02 0 0 .02
0
0 .03
[1] 2lbd.a .02 .03 .01 .01 .02 0
0
.04
[1] 5m24.a .04 .05 .04 .04 .04 .03 .04
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 0.4 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
1exa.a
1exx.a
1fcx.a
1fcy.a
1fcz.a
1fd0.a
2lbd.a
5m24.a
[1] 1exa.a
0
0.2 0.2 0.2 0.2 0.2 0.2 0.3
[1] 1exx.a 0.2
0
0.2 0.3 0.2 0.2 0.3 0.4
[1] 1fcx.a 0.2 0.2
0
0.1 0.1 0.1 0.2 0.4
[1] 1fcy.a 0.2 0.3 0.1
0
0.1 0.2 0.2 0.3
[1] 1fcz.a 0.2 0.2 0.1 0.1
0
0.2 0.2 0.3
[1] 1fd0.a 0.2 0.2 0.1 0.2 0.2
0
0.2 0.3
[1] 2lbd.a 0.2 0.3 0.2 0.2 0.2 0.2
0
0.3
[1] 5m24.a 0.3 0.4 0.4 0.3 0.3 0.3 0.3
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
1exa.a
1exx.a
1fcx.a
1fcy.a
1fcz.a
1fd0.a
2lbd.a
5m24.a
[1] 1exa.a
0
0.2 0.4 0.4 0.3 0.3 0.8 0.6
[1] 1exx.a 0.2
0
0.4 0.4 0.3 0.3 0.8 0.6
[1] 1fcx.a 0.4 0.4
0
0.2 0.3 0.2 0.8 0.7
[1] 1fcy.a 0.4 0.4 0.2
0
0.3 0.2 0.8 0.6
[1] 1fcz.a 0.3 0.3 0.3 0.3
0
0.3 0.8 0.6
[1] 1fd0.a 0.3 0.3 0.2 0.2 0.3
0
0.8 0.6
[1] 2lbd.a 0.8 0.8 0.8 0.8 0.8 0.8
0
0.8
[1] 5m24.a 0.6 0.6 0.7 0.6 0.6 0.6 0.8
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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

loading...