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VDRA_DANRE_155_453_coactiv

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

Composition of the binding site

Protein chains homotetramer [domain annotation]
A1 (VDRA_DANRE):D: NR LBD (267, 270, 274, 279, 280, 284, 287, 288, 291, 292, 442, 443, 446, 447)
R: Interaction with coactivator LXXLL motif (274, 279, 280, 284, 287, 288, 291, 292)
451:453
267, 270, 274, 279, 280, 284, 287, 288, 291, 292, 442, 443, 446, 447, 451:453
A2 (VDRA_DANRE):D: NR LBD (431, 432, 434, 435, 437, 438)431, 432, 434, 435, 437, 438
A3 (VDRA_DANRE):D: NR LBD (399, 400)399, 400
A4 (VDRA_DANRE):D: NR LBD (396:398, 400, 401, 403)
R: Hinge (153:155)
153:155, 396:398, 400, 401, 403

Full PDB list

2hbh, 2hc4, 2hcd, 3dr1, 3o1d, 3o1e, 4fhh, 4fhi, 4g1d, 4g1y, 4g1z, 4g20, 4g21, 4g2h, 4ia1, 4ia2, 4ia3, 4ia7, 4q0a, 4ruj, 4ruo, 4rup, 5e7v, 5lga, 5mx7, 5nky, 5nma, 5nmb (redundant Pocketome entry)

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1 A2 A4
I
2
7
0
K
2
7
4
F
2
7
9
R
2
8
0
A
2
8
4
Q
2
8
7
I
2
8
8
L
2
9
1
K
2
9
2
P
4
4
2
L
4
4
3
E
4
4
6
V
4
4
7
E
4
5
1
V
4
5
2
S
4
3
1
F
4
3
2
P
4
3
4
E
4
3
5
S
4
3
7
M
4
3
8
K
1
5
3
P
1
5
4
R
1
5
5
I
3
9
7
Q
3
9
8
R
4
0
3
[1]3dr1.a RHKILHRLLQE91 . . . . . . . . . . . . . . . . . . . . . S H M . . .
[1]4fhi.a KHKILHRLLQ81 . . . . . . . . . . . . . . . . . . . . . - - M . . .
[1]4g1d.a RHKILHRLLQE90 . . . . . . . . . . . . . . . . . . . . . - H M . . .
[1]4g1z.a RHKILHRLLQ85 . . . . . . . . . . . . . . . . . . . . . - H M . . .
[1]4g20.a RHKILHRLLQ85 . . . . . . . . . . . . . . . . . . . . . - - - . . .
[1]4q0a.c GHKILHRLLQ86 . . . . . . . . . . . . . . . . . . . . . - - - - - -
[1]5lga.a KHKILHRLLQ85 . . . . . . . . . . . . . . . . . . . . . - H M . . .
[1]5nmb.2 RHKILHRLLQE93 . . . . . . . . . . . . . . . . . . . . . - - - - - -

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 A3 A4
Q
2
6
7
I
2
7
0
K
2
7
4
F
2
7
9
R
2
8
0
A
2
8
4
Q
2
8
7
I
2
8
8
L
2
9
1
K
2
9
2
P
4
4
2
L
4
4
3
E
4
4
6
V
4
4
7
E
4
5
1
V
4
5
2
S
4
5
3
S
4
3
1
F
4
3
2
P
4
3
4
E
4
3
5
S
4
3
7
M
4
3
8
H
3
9
9
P
4
0
0
K
1
5
3
P
1
5
4
R
1
5
5
R
3
9
6
I
3
9
7
Q
3
9
8
P
4
0
0
G
4
0
1
R
4
0
3
[1]3dr1.a . . . . . . . . . . . . . . * . - . . . . . . - - S H M . . . . . .
[1]4fhi.a . . . . * . . . . . . . . . . . - . . . . . . . . - - M . . . . . .
[1]4g1d.a . . . . * . . . . . . . . . . . - . . . . . . . . - H M . . . . . .
[1]4g1z.a . . . . . . . . . . . . . . . . - . . . . . . . . - H M . . . . . .
[1]4g20.a . . . . * . . . . . . . . . . . - . . . . . . . . - - - . . . . . .
[1]4q0a.c . . . . * . . . . . . . . . . . . . . . . . . . . - - - - - - - - -
[1]5lga.a . . . . . . . . . . . . . . . . - . . . . . . . . - H M . . . . . .
[1]5nmb.2 . . . . . . . . . . . . . . . . - . . . . . . . . - - - - - - - - -

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
3dr1.a:RHKILHRLLQE
4fhi.a:KHKILHRLLQ
4g1d.a:RHKILHRLLQE
4g1z.a:RHKILHRLLQ
4g20.a:RHKILHRLLQ
4q0a.c:GHKILHRLLQ
5lga.a:KHKILHRLLQ
5nmb.2:RHKILHRLLQE
[1] 3dr1.a
0.1
0.1 0 0.1 0.1 0 0.1 1.5
[1] 4fhi.a 2.5
0.1
0.1 0.2 0.3 0.1 0 0.3
[1] 4g1d.a 2.5 0
0.3
0.2 0.3 0.1 0 0.2
[1] 4g1z.a 0 0 0.3
0.2
0.3 0 0 0.3
[1] 4g20.a 1.9 0.4 0.1 0.1
0
0.1 0 0.5
[1] 4q0a.c 1.0 0.3 0.1 0.2 0.2
0
0.1 0.3
[1] 5lga.a 0.2 0.2 0.3 0.3 0.4 0.1
0
0.5
[1] 5nmb.2 0.1 0.1 0.1 0.1 0.1 0.1 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
3dr1.a
4fhi.a
4g1d.a
4g1z.a
4g20.a
4q0a.c
5lga.a
5nmb.2
[1] 3dr1.a
0
.11 .12 .06 .11 .07 .06 .05
[1] 4fhi.a .11
0
.02 .09 .06 .06 .10 .09
[1] 4g1d.a .12 .02
0
.07 .04 .06 .08 .08
[1] 4g1z.a .06 .09 .07
0
.07 .05 .01 .02
[1] 4g20.a .11 .06 .04 .07
0
.04 .08 .07
[1] 4q0a.c .07 .06 .06 .05 .04
0
.06 .04
[1] 5lga.a .06 .10 .08 .01 .08 .06
0
.03
[1] 5nmb.2 .05 .09 .08 .02 .07 .04 .03
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 0.9 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
3dr1.a
4fhi.a
4g1d.a
4g1z.a
4g20.a
4q0a.c
5lga.a
5nmb.2
[1] 3dr1.a
0
0.6 0.7 0.6 0.7 0.7 0.7 0.6
[1] 4fhi.a 0.6
0
0.6 0.5 0.6 0.8 0.5 0.4
[1] 4g1d.a 0.7 0.6
0
0.4 0.4 0.6 0.5 0.6
[1] 4g1z.a 0.6 0.5 0.4
0
0.3 0.5 0.5 0.5
[1] 4g20.a 0.7 0.6 0.4 0.3
0
0.5 0.4 0.5
[1] 4q0a.c 0.7 0.8 0.6 0.5 0.5
0
0.6 0.7
[1] 5lga.a 0.7 0.5 0.5 0.5 0.4 0.6
0
0.5
[1] 5nmb.2 0.6 0.4 0.6 0.5 0.5 0.7 0.5
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 0.5 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
3dr1.a
4fhi.a
4g1d.a
4g1z.a
4g20.a
4q0a.c
5lga.a
5nmb.2
[1] 3dr1.a
0
0.8 1.3 1.1 1.0 1.0 1.0 0.6
[1] 4fhi.a 0.8
0
0.7 0.7 0.8 1.1 0.9 1.0
[1] 4g1d.a 1.3 0.7
0
0.5 0.6 0.9 1.3 1.1
[1] 4g1z.a 1.1 0.7 0.5
0
0.4 0.7 1.1 0.7
[1] 4g20.a 1.0 0.8 0.6 0.4
0
0.8 0.9 1.1
[1] 4q0a.c 1.0 1.1 0.9 0.7 0.8
0
1.1 1.1
[1] 5lga.a 1.0 0.9 1.3 1.1 0.9 1.1
0
1.2
[1] 5nmb.2 0.6 1.0 1.1 0.7 1.1 1.1 1.2
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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