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STF1_HUMAN_220_461_coactiv

Steroidogenic factor 1 [Nuclear hormone receptor family. NR5 subfamily]

Composition of the binding site

Protein chains monomer [domain annotation]
A1 (STF1_HUMAN):D: NR LBD (273, 274, 277, 281, 286, 291, 294, 295, 298, 299, 448:452, 454, 455, 458, 459)
R: Important for dimerization (273, 274, 277, 281, 286, 291, 294, 295, 298, 299, 448:452, 454, 455, 458:460)
273, 274, 277, 281, 286, 291, 294, 295, 298, 299, 448:452, 454, 455, 458:460

Full PDB list

1ymt, 1yow, 1yp0, 1zdt, 3f7d, 4qjr, 4qk4 (redundant Pocketome entry)

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1
F
2
7
3
I
2
7
4
V
2
7
7
R
2
8
1
F
2
8
6
V
2
9
1
Q
2
9
4
M
2
9
5
L
2
9
8
Q
2
9
9
R
4
4
8
N
4
4
9
N
4
5
0
L
4
5
1
E
4
5
4
M
4
5
5
A
4
5
8
Q
4
6
0
[1]1ymt.a RPTILYALLS80 . . . . . . . . . . . . . . . . . -
[1]1yow.a AQALAALLAKA73 . . . . . . . . . . . . . . . . . -
[1]1zdt.a ENALLRYLLDKD102 . . . . . . . . . . . . . . . . . .
[1]1zdt.b ENALLRYLLDK94 . . . . . . . . . . . . . . . . . -
[1]4qk4.a PSLLKKLLLAPA88 . . . . . . . . . . . . . . . . . .
[2]3f7d.a PSLLKKLLLA76 . . . . . . . . . . . . . . . . . .
[3]1yp0.a HPTILYTLLSPG90 . . . . . . . . . . . . . . . . . .

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
2
7
3
I
2
7
4
V
2
7
7
R
2
8
1
F
2
8
6
V
2
9
1
Q
2
9
4
M
2
9
5
L
2
9
8
Q
2
9
9
R
4
4
8
N
4
4
9
N
4
5
0
L
4
5
1
L
4
5
2
E
4
5
4
M
4
5
5
A
4
5
8
K
4
5
9
Q
4
6
0
[1]1ymt.a . . . * . . . . . . . . . * . . . . - -
[1]1yow.a . . . . . . . . . . . . . . . . . . - -
[1]1zdt.a . . . * . . . . . . . . . . . . . . . .
[1]1zdt.b . . . . . . . . . . . . . . . . . . . -
[1]4qk4.a . . . . . . . . . . . . . * . . . . . .
[2]3f7d.a . . . * . . . . . . * . . * . * . . . .
[3]1yp0.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
1ymt.a:RPTILYALLS
1yow.a:AQALAALLAKA
1zdt.a:ENALLRYLLDKD
1zdt.b:ENALLRYLLDK
4qk4.a:PSLLKKLLLAPA
3f7d.a:PSLLKKLLLA
1yp0.a:HPTILYTLLSPG
[1] 1ymt.a
0
0.3 1.7 0.7 0 0.1 0
[1] 1yow.a 0.6
0.2
0.6 0.1 0.2 0.4 0.6
[1] 1zdt.a 0.5 0.3
0
1.0 0.2 0.5 0.5
[1] 1zdt.b 0 0.1 0.2
0
0.1 0.1 0
[1] 4qk4.a 0 0.7 2.2 1.0
0
0.1 0
[2] 3f7d.a 1.1 2.5 4.4 2.1 0.7
0.1
0.9
[3] 1yp0.a 0.9 1.5 6.9 5.0 0 0.1
0
[Pocket-ligand steric clashes matrix]

Pocket clash dissimilarity (3 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
1ymt.a
1yow.a
1zdt.a
1zdt.b
4qk4.a
3f7d.a
1yp0.a
[1] 1ymt.a
0
.08 .08 .11 .05 .22 .31
[1] 1yow.a .08
0
.08 .06 .11 .29 .38
[1] 1zdt.a .08 .08
0
.08 .12 .26 .37
[1] 1zdt.b .11 .06 .08
0
.13 .31 .40
[1] 4qk4.a .05 .11 .12 .13
0
.21 .32
[2] 3f7d.a .22 .29 .26 .31 .21
0
.49
[3] 1yp0.a .31 .38 .37 .40 .32 .49
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
1ymt.a
1yow.a
1zdt.a
1zdt.b
4qk4.a
3f7d.a
1yp0.a
[1] 1ymt.a
0
0.9 1.1 0.6 0.3 2.3 0.4
[1] 1yow.a 0.9
0
0.8 0.6 1.1 2.6 1.0
[1] 1zdt.a 1.1 0.8
0
1.0 1.4 2.9 2.7
[1] 1zdt.b 0.6 0.6 1.0
0
1.0 2.4 1.5
[1] 4qk4.a 0.3 1.1 1.4 1.0
0
2.2 2.5
[2] 3f7d.a 2.3 2.6 2.9 2.4 2.2
0
3.0
[3] 1yp0.a 0.4 1.0 2.7 1.5 2.5 3.0
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 1.0 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
1ymt.a
1yow.a
1zdt.a
1zdt.b
4qk4.a
3f7d.a
1yp0.a
[1] 1ymt.a
0
1.8 1.8 1.3 1.2 3.1 1.1
[1] 1yow.a 1.8
0
1.6 2.1 2.2 4.1 2.2
[1] 1zdt.a 1.8 1.6
0
2.3 2.1 3.9 3.0
[1] 1zdt.b 1.3 2.1 2.3
0
1.9 3.1 2.3
[1] 4qk4.a 1.2 2.2 2.1 1.9
0
3.0 3.1
[2] 3f7d.a 3.1 4.1 3.9 3.1 3.0
0
3.7
[3] 1yp0.a 1.1 2.2 3.0 2.3 3.1 3.7
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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