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VDR_RAT_116_422_coactiv

Vitamin D3 receptor [Nuclear hormone receptor family. NR1 subfamily]

Composition of the binding site

Protein chains homodimer [domain annotation]
A1 (VDR_RAT):D: NR LBD (235, 238, 242, 247, 248, 252, 253, 255:257, 259, 260, 412, 413, 416, 417, 419)
R: Interaction with coactivator LXXLL motif (242, 247, 248, 252, 253, 255:257, 259, 260)
420
235, 238, 242, 247, 248, 252, 253, 255:257, 259, 260, 412, 413, 416, 417, 419, 420
A2 (VDR_RAT):D: NR LBD (403:405, 407, 408, 415)403:405, 407, 408, 415

Full PDB list

2zl9, 2zla, 2zlc, 2zmh, 2zmi, 2zmj, 2zxm, 2zxn, 3afr, 3vjs, 3vjt, 3vrt, 3vru, 3vrv, 3vrw, 3vt3, 3vt4, 3vt5, 3vt6, 3vt7, 3vt8, 3vt9, 3vtb, 3vtc, 3vtd, 3w0h, 3w5p, 3w5q, 3w5r, 3w5t, 3wt5, 3wt6, 3wt7, 3wtq, 4ynk, 5awj, 5awk, 5b41, 5b5b, 5h1e (redundant Pocketome entry)

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1 A2
I
2
3
8
K
2
4
2
F
2
4
7
R
2
4
8
S
2
5
2
D
2
5
3
Q
2
5
5
I
2
5
6
L
2
5
9
K
2
6
0
P
4
1
2
L
4
1
3
E
4
1
6
Q
4
0
3
P
4
0
4
E
4
0
5
S
4
0
7
M
4
0
8
L
4
1
5
[1]2zl9.a NHPMLMNLLK82 . . . . . . . . . . . . . . . . . . .
[1]3vtb.a KNHPMLMNLLK91 . . . . . . . . . . . . . . . . . . .
[1]3w0h.a NHPMLMNLLKD90 . . . . . . . . . . . . . . . . . . .
[1]5h1e.a ENALLRYLLD85 . . . . . . . . . . . . . . . . . . .

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 A2
Q
2
3
5
I
2
3
8
K
2
4
2
F
2
4
7
R
2
4
8
S
2
5
2
D
2
5
3
Q
2
5
5
I
2
5
6
V
2
5
7
L
2
5
9
K
2
6
0
P
4
1
2
L
4
1
3
E
4
1
6
V
4
1
7
G
4
1
9
N
4
2
0
Q
4
0
3
P
4
0
4
E
4
0
5
S
4
0
7
M
4
0
8
L
4
1
5
[1]2zl9.a . . . . . . . . . . . . . . . . . - . . . . . .
[1]3vtb.a . . . . . . . . . . . . . . . . . . . . . . . .
[1]3w0h.a . . . . . . . . . . . . . . . . . . . . . . . .
[1]5h1e.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
2zl9.a:NHPMLMNLLK
3vtb.a:KNHPMLMNLLK
3w0h.a:NHPMLMNLLKD
5h1e.a:ENALLRYLLD
[1] 2zl9.a
0
0 0.1 0.5
[1] 3vtb.a 0.3
0.1
0 0.2
[1] 3w0h.a 0.5 0.4
0.1
0.4
[1] 5h1e.a 0.4 0.3 0.1
0.5
[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
2zl9.a
3vtb.a
3w0h.a
5h1e.a
[1] 2zl9.a
0
.02 .03 .02
[1] 3vtb.a .02
0
.02 .03
[1] 3w0h.a .03 .02
0
.03
[1] 5h1e.a .02 .03 .03
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 0.8 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
2zl9.a
3vtb.a
3w0h.a
5h1e.a
[1] 2zl9.a
0
0.4 0.7 0.4
[1] 3vtb.a 0.4
0
0.9 0.4
[1] 3w0h.a 0.7 0.9
0
0.7
[1] 5h1e.a 0.4 0.4 0.7
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

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
2zl9.a
3vtb.a
3w0h.a
5h1e.a
[1] 2zl9.a
0
0.5 1.6 0.8
[1] 3vtb.a 0.5
0
1.6 0.8
[1] 3w0h.a 1.6 1.6
0
1.6
[1] 5h1e.a 0.8 0.8 1.6
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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