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NR5A2_MOUSE_316_559_pep

Nuclear receptor subfamily 5 group A member 2 [Nuclear hormone receptor family. NR5 subfamily]

Composition of the binding site

Protein chains monomer [domain annotation]
A1 (NR5A2_MOUSE):D: NR LBD (373, 376, 380, 390, 391, 393:395, 397, 398, 484, 547:550, 553, 554)373, 376, 380, 390, 391, 393:395, 397, 398, 484, 547:550, 553, 554

Full PDB list

1pk5, 1zh7, 3f5c

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1
F
3
7
3
V
3
7
6
R
3
8
0
V
3
9
0
D
3
9
1
Q
3
9
3
M
3
9
4
K
3
9
5
L
3
9
7
Q
3
9
8
E
4
8
4
N
5
4
8
N
5
4
9
L
5
5
0
E
5
5
3
M
5
5
4
[1]1pk5.a none . . . . . . . . . . . . . . . .
[1]1zh7.a SHPTILYTLLS88 . . . . . . . . . . . . . . . .
[2]3f5c.a LPCFQILPLDQQ-CVKYIEGL161 . . . . . . . . . . . . . . . .

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
7
3
V
3
7
6
R
3
8
0
V
3
9
0
D
3
9
1
Q
3
9
3
M
3
9
4
K
3
9
5
L
3
9
7
Q
3
9
8
E
4
8
4
Y
5
4
7
N
5
4
8
N
5
4
9
L
5
5
0
E
5
5
3
M
5
5
4
[1]1pk5.a . . * . . . * . . . . . . * . * .
[1]1zh7.a . . . . . . . . . . . . . * . . .
[2]3f5c.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
1pk5.a is apo
1zh7.a:SHPTILYTLLS
3f5c.a:LPCFQILPLDQQ-CVKYIEGL
[1] 1pk5.a
-
4.7 4.4
[1] 1zh7.a -
0.2
4.5
[2] 3f5c.a - 2.4
0.1
[Pocket-ligand steric clashes matrix]

Pocket clash dissimilarity (2 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
1pk5.a
1zh7.a
3f5c.a
[1] 1pk5.a
0
.23 .35
[1] 1zh7.a .23
0
.34
[2] 3f5c.a .35 .34
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 1.6 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
1pk5.a
1zh7.a
3f5c.a
[1] 1pk5.a
0
0.6 1.5
[1] 1zh7.a 0.6
0
1.5
[2] 3f5c.a 1.5 1.5
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 0.6 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
1pk5.a
1zh7.a
3f5c.a
[1] 1pk5.a
0
1.6 2.7
[1] 1zh7.a 1.6
0
2.7
[2] 3f5c.a 2.7 2.7
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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