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CTDS1_HUMAN_76_258

Carboxy-terminal domain RNA polymerase II polypeptide A small phosphatase 1

Composition of the binding site

Protein chains monomer [domain annotation]
A1 (CTDS1_HUMAN):D: FCP1 homology (96:98, 104:107, 118, 120, 121, 125, 127, 152:155, 157, 158, 178, 187, 188, 190, 208, 210, 211)96:98, 104:107, 118, 120, 121, 125, 127, 152:155, 157, 158, 178, 187, 188, 190, 208, 210, 211
Metals (Me):Mg

Full PDB list

1t9z, 1ta0, 2ghq, 2ght, 3l0b, 3l0c, 3l0y, 3pgl, 4ygy, 4yh1 (redundant Pocketome entry)

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1 Me
D
9
6
L
9
7
D
9
8
S
1
0
4
S
1
0
5
F
1
0
6
K
1
0
7
V
1
1
8
I
1
2
0
D
1
2
1
H
1
2
5
T
1
5
2
A
1
5
3
S
1
5
4
L
1
5
5
K
1
5
7
Y
1
5
8
R
1
7
8
N
1
8
7
Y
1
8
8
K
1
9
0
S
2
0
8
[1]1ta0.a none * . . . . . . . . . . . . . . . . . . . . . Mg
[1]2ghq.a sepPTsepP41 N . . . . . . . . . . . . . . . . . . . . . Mg
[1]2ghq.b PSYsepPTsepPS73 N . . . . . . . . . . . . . . . . . . . . . Mg
[1]2ght.a SPTsepP37 N . . . . . . . . . . . . . . . . . . . . . Mg
[1]2ght.b SYSPTsepPS62 N . . . . . . . . . . . . . . . . . . . . . Mg
[1]3l0b.a 1pg17 * . . . . . . . . . . . . . . . . . . . . . Mg
[1]3l0b.b none * . . . . . . . . . . . . . . . . . . . . .
[1]3l0c.b none . . . . . . . . . . . . . . . . . . . . . . Mg
[1]3l0y.b none . . A . . . . . . . . . . . . . . . . . . . Mg
[1]3pgl.a rzx25 . . . . . . . . . . . . . . . . . . . . . . Mg
[1]4yh1.a SPT4cg36 N . . . . . . . . . . . . . . . . . . . . . Mg

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 Me
D
9
6
L
9
7
D
9
8
S
1
0
4
S
1
0
5
F
1
0
6
K
1
0
7
V
1
1
8
I
1
2
0
D
1
2
1
H
1
2
5
V
1
2
7
T
1
5
2
A
1
5
3
S
1
5
4
L
1
5
5
K
1
5
7
Y
1
5
8
R
1
7
8
N
1
8
7
Y
1
8
8
K
1
9
0
S
2
0
8
A
2
1
0
S
2
1
1
[1]1ta0.a bfd . . . . . . . . * . . . . . . . . . . . . . . . Mg
[1]2ghq.a N . . . . . . . . . . . . . . . * . . . . . . . . Mg
[1]2ghq.b N . . . . . . . . . . . . . . . . . . . . . . . . Mg
[1]2ght.a N . . . . . . . . . . . . . . . . . . . . . . . . Mg
[1]2ght.b N . . . . . . . . . . . . . . . . . . . . . . . . Mg
[1]3l0b.a phd . . . . . . . . . . . . . . . . . . . . . . . . Mg
[1]3l0b.b * . . . . . . . . . . . . . . . . . . . . . . . .
[1]3l0c.b . . . . . . . . . . . . . . . . . . . . . . . . . Mg
[1]3l0y.b . . A . . . . . . . . . . . . . * * . . . . . . . Mg
[1]3pgl.a . . . . . . . . . . . . . . . . . . . . . . . . . Mg
[1]4yh1.a N . . . . . . . . . . . . . . . . . . . . . . . . Mg

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
1ta0.a is apo
2ghq.a:sepPTsepP
2ghq.b:PSYsepPTsepPS
2ght.a:SPTsepP
2ght.b:SYSPTsepPS
3l0b.a:1pg
3l0b.b is apo
3l0c.b is apo
3l0y.b is apo
3pgl.a:rzx
4yh1.a:SPT4cg
[1] 1ta0.a
-
3.0 4.9 3.0 4.4 0 - - - 0 2.6
[1] 2ghq.a -
0
0.8 0.2 0.5 0 - - - 0 0.2
[1] 2ghq.b - 0.2
0.3
0.1 0.1 0 - - - 0.1 0.2
[1] 2ght.a - 0.2 0.6
0.1
0.4 0 - - - 0 0.2
[1] 2ght.b - 0.3 0.9 0.3
0.2
0 - - - 0.1 0.3
[1] 3l0b.a - 3.2 4.1 3.2 3.5
0
- - - 0 2.9
[1] 3l0b.b - 0.1 0.4 0.1 0.4 0
-
- - 0 0.1
[1] 3l0c.b - 0 0.8 0.1 0.4 0 -
-
- 0 0.2
[1] 3l0y.b - 3.1 4.9 3.1 4.5 3.3 - -
-
3.5 3.5
[1] 3pgl.a - 1.1 1.8 1.2 0.8 0 - - -
0.1
0.7
[1] 4yh1.a - 0.2 0.8 0.1 0.4 0 - - - 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
1ta0.a
2ghq.a
2ghq.b
2ght.a
2ght.b
3l0b.a
3l0b.b
3l0c.b
3l0y.b
3pgl.a
4yh1.a
[1] 1ta0.a
0
.20 .21 .20 .20 .09 .20 .20 .34 .22 .19
[1] 2ghq.a .20
0
.04 .02 .02 .16 .02 .03 .18 .07 .03
[1] 2ghq.b .21 .04
0
.02 .02 .16 .02 .04 .21 .06 .03
[1] 2ght.a .20 .02 .02
0
.02 .16 .02 .03 .20 .06 .01
[1] 2ght.b .20 .02 .02 .02
0
.15 .02 .03 .20 .05 .02
[1] 3l0b.a .09 .16 .16 .16 .15
0
.16 .16 .30 .13 .15
[1] 3l0b.b .20 .02 .02 .02 .02 .16
0
.02 .19 .06 .02
[1] 3l0c.b .20 .03 .04 .03 .03 .16 .02
0
.19 .06 .02
[1] 3l0y.b .34 .18 .21 .20 .20 .30 .19 .19
0
.23 .19
[1] 3pgl.a .22 .07 .06 .06 .05 .13 .06 .06 .23
0
.05
[1] 4yh1.a .19 .03 .03 .01 .02 .15 .02 .02 .19 .05
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
1ta0.a
2ghq.a
2ghq.b
2ght.a
2ght.b
3l0b.a
3l0b.b
3l0c.b
3l0y.b
3pgl.a
4yh1.a
[1] 1ta0.a
0
0.4 0.5 0.5 0.6 0.6 0.5 0.6 0.5 0.5 0.5
[1] 2ghq.a 0.4
0
0.4 0.2 0.4 0.5 0.3 0.4 0.4 0.4 0.2
[1] 2ghq.b 0.5 0.4
0
0.4 0.1 0.3 0.5 0.6 0.6 0.3 0.5
[1] 2ght.a 0.5 0.2 0.4
0
0.4 0.5 0.3 0.4 0.4 0.5 0.2
[1] 2ght.b 0.6 0.4 0.1 0.4
0
0.3 0.4 0.6 0.6 0.3 0.5
[1] 3l0b.a 0.6 0.5 0.3 0.5 0.3
0
0.4 0.5 0.6 0.3 0.5
[1] 3l0b.b 0.5 0.3 0.5 0.3 0.4 0.4
0
0.2 0.4 0.4 0.3
[1] 3l0c.b 0.6 0.4 0.6 0.4 0.6 0.5 0.2
0
0.5 0.6 0.3
[1] 3l0y.b 0.5 0.4 0.6 0.4 0.6 0.6 0.4 0.5
0
0.5 0.3
[1] 3pgl.a 0.5 0.4 0.3 0.5 0.3 0.3 0.4 0.6 0.5
0
0.5
[1] 4yh1.a 0.5 0.2 0.5 0.2 0.5 0.5 0.3 0.3 0.3 0.5
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

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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
1ta0.a
2ghq.a
2ghq.b
2ght.a
2ght.b
3l0b.a
3l0b.b
3l0c.b
3l0y.b
3pgl.a
4yh1.a
[1] 1ta0.a
0
0.8 0.9 1.0 0.9 1.0 0.9 1.0 1.3 0.9 0.9
[1] 2ghq.a 0.8
0
0.8 0.5 0.7 1.1 0.7 0.6 1.3 0.9 0.5
[1] 2ghq.b 0.9 0.8
0
0.8 0.6 0.9 0.8 0.9 1.4 0.7 0.9
[1] 2ght.a 1.0 0.5 0.8
0
0.8 1.1 0.7 0.6 1.3 0.9 0.4
[1] 2ght.b 0.9 0.7 0.6 0.8
0
0.9 0.8 0.9 1.4 0.6 0.8
[1] 3l0b.a 1.0 1.1 0.9 1.1 0.9
0
1.0 1.1 1.6 0.7 1.2
[1] 3l0b.b 0.9 0.7 0.8 0.7 0.8 1.0
0
0.6 1.3 0.9 0.7
[1] 3l0c.b 1.0 0.6 0.9 0.6 0.9 1.1 0.6
0
1.3 1.0 0.6
[1] 3l0y.b 1.3 1.3 1.4 1.3 1.4 1.6 1.3 1.3
0
1.4 1.3
[1] 3pgl.a 0.9 0.9 0.7 0.9 0.6 0.7 0.9 1.0 1.4
0
0.9
[1] 4yh1.a 0.9 0.5 0.9 0.4 0.8 1.2 0.7 0.6 1.3 0.9
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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