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RXRB_HUMAN_289_527_coactiv

Retinoic acid receptor RXR-beta [Nuclear hormone receptor family. NR2 subfamily]

Composition of the binding site

Protein chains monomer [domain annotation]
A1 (RXRB_HUMAN):D: NR LBD (348, 351, 355, 365, 368, 369, 372, 373, 520, 521, 524, 525, 527:529)
530:533
348, 351, 355, 365, 368, 369, 372, 373, 520, 521, 524, 525, 527:533

Full PDB list

1h9u, 1uhl, 5hjp, 5i4v, 5kya, 5kyj

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1
F
3
4
8
V
3
5
1
K
3
5
5
L
3
6
5
Q
3
6
8
V
3
6
9
L
3
7
2
R
3
7
3
T
5
2
0
F
5
2
1
E
5
2
4
[1]5i4v.f none . . . . . . . . . . .
[1]5kya.b none . . . . . . . . . . .
[1]5kya.f none . . . . . . . . . . .
[2]1h9u.a none . . . . . . . . . . -
[2]1uhl.a HKILHRLLQ81 . . . . . . . . . . .
[3]5hjp.a none . . . . . . . . . . .
[4]5kyj.b 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
F
3
4
8
V
3
5
1
K
3
5
5
L
3
6
5
Q
3
6
8
V
3
6
9
L
3
7
2
R
3
7
3
T
5
2
0
F
5
2
1
E
5
2
4
M
5
2
5
.
5
2
7
B
A
5
2
8
P
5
2
9
H
5
3
0
Q
5
3
1
L
5
3
2
A
5
3
3
.
5
3
3
A
.
5
3
3
B
.
5
3
3
C
.
5
3
3
D
.
5
3
3
E
.
5
3
3
F
[1]5i4v.f . . . . . . . . . . . . - G S * K I L H R L L Q D
[1]5kya.b . . . . . . . . . . . . - . S * K I L H R L L Q -
[1]5kya.f . . . . . . . . . . . . - G S * K I L H R L L Q -
[2]1h9u.a . . . . . . . . . . - - - - - - - - - - - - - - -
[2]1uhl.a . . . . . . . . . . . . - . - - - - - - - - - - -
[3]5hjp.a . . . . . . . . . . . . K I L * R * L Q - - - - -
[4]5kyj.b . . . . . . . . . . . . - . H K I * H R L L Q - -

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
5i4v.f is apo
5kya.b is apo
5kya.f is apo
1h9u.a is apo
1uhl.a:HKILHRLLQ
5hjp.a is apo
5kyj.b is apo
[1] 5i4v.f
-
- - - 57 - -
[1] 5kya.b -
-
- - 55 - -
[1] 5kya.f - -
-
- 54 - -
[2] 1h9u.a - - -
-
0.2 - -
[2] 1uhl.a - - - -
0.1
- -
[3] 5hjp.a - - - - 42
-
-
[4] 5kyj.b - - - - 53 -
-
[Pocket-ligand steric clashes matrix]

Pocket clash dissimilarity (4 clusters)

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
5i4v.f
5kya.b
5kya.f
1h9u.a
1uhl.a
5hjp.a
5kyj.b
[1] 5i4v.f
0
.13 .16 2.3 2.3 1.9 .49
[1] 5kya.b .13
0
.09 2.2 2.2 1.8 .48
[1] 5kya.f .16 .09
0
2.2 2.2 1.8 .50
[2] 1h9u.a 2.3 2.2 2.2
0
.01 1.7 2.1
[2] 1uhl.a 2.3 2.2 2.2 .01
0
1.7 2.1
[3] 5hjp.a 1.9 1.8 1.8 1.7 1.7
0
1.5
[4] 5kyj.b .49 .48 .50 2.1 2.1 1.5
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 3.1 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
5i4v.f
5kya.b
5kya.f
1h9u.a
1uhl.a
5hjp.a
5kyj.b
[1] 5i4v.f
0
2.0 0.7 11 2.9 4.4 3.0
[1] 5kya.b 2.0
0
1.9 11 0.7 4.9 2.1
[1] 5kya.f 0.7 1.9
0
11 2.9 4.7 3.0
[2] 1h9u.a 11 11 11
0
11 11 11
[2] 1uhl.a 2.9 0.7 2.9 11
0
3.9 0.5
[3] 5hjp.a 4.4 4.9 4.7 11 3.9
0
4.4
[4] 5kyj.b 3.0 2.1 3.0 11 0.5 4.4
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 3.0 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
5i4v.f
5kya.b
5kya.f
1h9u.a
1uhl.a
5hjp.a
5kyj.b
[1] 5i4v.f
0
1.6 0.7 9.4 2.2 4.4 3.1
[1] 5kya.b 1.6
0
1.5 9.5 1.0 4.7 2.6
[1] 5kya.f 0.7 1.5
0
9.5 2.2 4.5 3.1
[2] 1h9u.a 9.4 9.5 9.5
0
9.5 9.5 9.5
[2] 1uhl.a 2.2 1.0 2.2 9.5
0
3.2 0.9
[3] 5hjp.a 4.4 4.7 4.5 9.5 3.2
0
4.2
[4] 5kyj.b 3.1 2.6 3.1 9.5 0.9 4.2
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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