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ECR_HELVI_304_550

Ecdysone receptor [Nuclear hormone receptor family. NR1 subfamily]

Composition of the binding site

Protein chains monomer [domain annotation]
A1 (ECR_HELVI):D: NR LBD (330:332, 354, 357, 358, 360, 361, 364, 395, 398, 399, 401, 402, 405, 413:416, 418, 420, 421, 426, 431, 434, 437, 438, 518, 521, 522, 525, 526, 529, 540, 544)330:332, 354, 357, 358, 360, 361, 364, 395, 398, 399, 401, 402, 405, 413:416, 418, 420, 421, 426, 431, 434, 437, 438, 518, 521, 522, 525, 526, 529, 540, 544

Full PDB list

1r1k, 1r20, 2r40, 3ixp

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1
E
3
3
0
Q
3
3
1
P
3
3
2
F
3
5
4
I
3
5
7
T
3
5
8
M
3
6
0
T
3
6
1
T
3
6
4
S
3
9
5
M
3
9
8
M
3
9
9
R
4
0
1
V
4
0
2
R
4
0
5
V
4
1
3
L
4
1
4
F
4
1
5
A
4
1
6
Y
4
2
1
Y
4
2
6
M
4
3
1
V
4
3
4
D
4
3
7
L
4
3
8
L
5
1
8
Q
5
2
1
N
5
2
2
M
5
2
5
C
5
2
6
L
5
2
9
L
5
4
0
W
5
4
4
[1]1r1k.d p1a33 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]2r40.d 20e34 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[2]1r20.d hwg29 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[2]3ixp.d 83430 . . - . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

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
E
3
3
0
Q
3
3
1
P
3
3
2
F
3
5
4
I
3
5
7
T
3
5
8
M
3
6
0
T
3
6
1
T
3
6
4
S
3
9
5
M
3
9
8
M
3
9
9
R
4
0
1
V
4
0
2
R
4
0
5
V
4
1
3
L
4
1
4
F
4
1
5
A
4
1
6
N
4
1
8
A
4
2
0
Y
4
2
1
Y
4
2
6
M
4
3
1
V
4
3
4
D
4
3
7
L
4
3
8
L
5
1
8
Q
5
2
1
N
5
2
2
M
5
2
5
C
5
2
6
L
5
2
9
L
5
4
0
W
5
4
4
[1]1r1k.d . . . . . . . . . . . . . . . . . . . . . . . . * . . . . . . . . . .
[1]2r40.d . . . . . . . . . . * . . . . . . . . . . . . . * . . . . . . . . . .
[2]1r20.d . * . . . . . . . . . . . * . . . * . . . * . . . . . . . . . . . . .
[2]3ixp.d . . - . . . * . . . . . * . . . . * . . . * . . . . . . . . . . . . .

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
1r1k.d:p1a
2r40.d:20e
1r20.d:hwg
3ixp.d:834
[1] 1r1k.d
0.1
0.1 3.1 2.5
[1] 2r40.d 0
0
3.1 3.1
[2] 1r20.d 10 10
0.1
0.4
[2] 3ixp.d 9.1 10 0.4
0
[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
1r1k.d
2r40.d
1r20.d
3ixp.d
[1] 1r1k.d
0
.05 .38 .37
[1] 2r40.d .05
0
.39 .39
[2] 1r20.d .38 .39
0
.14
[2] 3ixp.d .37 .39 .14
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 2.1 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
1r1k.d
2r40.d
1r20.d
3ixp.d
[1] 1r1k.d
0
0.3 2.2 2.1
[1] 2r40.d 0.3
0
2.1 2.1
[2] 1r20.d 2.2 2.1
0
1.0
[2] 3ixp.d 2.1 2.1 1.0
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 1.5 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
1r1k.d
2r40.d
1r20.d
3ixp.d
[1] 1r1k.d
0
0.6 3.0 2.8
[1] 2r40.d 0.6
0
3.0 2.8
[2] 1r20.d 3.0 3.0
0
1.3
[2] 3ixp.d 2.8 2.8 1.3
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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