If you see this message after the page is completely loaded, then JavaScript is not supported or disabled in your browser. Please consider enabling JavaScript for this site.

AGO2_HUMAN_438_575

Protein argonaute-2 [Argonaute family. Ago subfamily]

Composition of the binding site

Protein chains monomer [domain annotation]
A1 (AGO2_HUMAN):D: Piwi (522, 524:526, 529, 533, 544:548, 551, 558, 559, 562, 563, 566, 570, 709, 710, 714, 753:761, 790, 792, 793, 795, 797, 798, 804, 808, 811, 812, 815)
R: Interaction with guide RNA (524:526, 529, 533, 544:548, 551, 558, 559, 562, 563, 566)
220:222, 358, 361, 364, 365, 368, 369, 375, 857:859
220:222, 358, 361, 364, 365, 368, 369, 375, 522, 524:526, 529, 533, 544:548, 551, 558, 559, 562, 563, 566, 570, 709, 710, 714, 753:761, 790, 792, 793, 795, 797, 798, 804, 808, 811, 812, 815, 857:859

Full PDB list

3luc, 3lud, 3lug, 3luh, 3luj, 3luk, 3qx8, 3qx9, 4f3t, 4ola, 4olb, 4w5n, 4w5o, 4w5q, 4w5r, 4w5t, 4z4c, 4z4d, 4z4e, 4z4f, 4z4g, 4z4h, 4z4i, 5js1, 5js2, 5ki6, 5t7b, 5wea (redundant Pocketome entry)

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1
D
3
5
8
I
3
6
5
A
3
6
9
L
5
2
2
G
5
2
4
K
5
2
5
T
5
2
6
Y
5
2
9
K
5
3
3
T
5
4
4
Q
5
4
5
C
5
4
6
V
5
4
7
Q
5
4
8
N
5
5
1
Q
5
5
8
T
5
5
9
N
5
6
2
L
5
6
3
K
5
6
6
K
5
7
0
K
7
0
9
R
7
1
0
R
7
1
4
H
7
5
3
I
7
5
6
Q
7
5
7
T
7
5
9
S
7
6
0
R
7
6
1
Y
7
9
0
R
7
9
2
C
7
9
3
R
7
9
5
V
7
9
7
S
7
9
8
Y
8
0
4
R
8
1
2
Y
8
1
5
[1]3luc.a none - - - . . . . . . . . . . . . . . . . . . - - - - - - - - - - - - - - - - - -
[1]3lud.a amp23 - - - . . . . . . . . . . . . . . . . . . - - - - - - - - - - - - - - - - - -
[1]3lug.a c5p5 - - - . . . . . . . . . . . . . . . . . . - - - - - - - - - - - - - - - - - -
[1]3luh.a 5gp5 - - - . . . . . . . . . . . . . . . . . . - - - - - - - - - - - - - - - - - -
[1]3luj.a u5p21 - - - . . . . . . . . . . . . . . . . . . - - - - - - - - - - - - - - - - - -
[1]3qx8.a gtg29 - - - . . . . . . . . . . . . . . . . . . - - - - - - - - - - - - - - - - - -
[1]3qx9.a atp31 - - - . . . . . . . . . . . . . . . . . . - - - - - - - - - - - - - - - - - -
[1]4f3t.a UAAAGU130 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]4olb.a AAAAAA133 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]4w5n.a UUCACAU145 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]4w5r.a UUCACA125 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]4w5t.a UUCACAUU165 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]5js1.a UUAUCU123 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]5js2.a 6op.f2t.6nw.uft.6oo.uft130 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]5ki6.a 6u0GGAGU141 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]5t7b.a uvpUAUAG129 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]5wea.a AAAAAAA155 - A . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

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
S
2
2
0
A
2
2
1
T
2
2
2
D
3
5
8
T
3
6
1
M
3
6
4
I
3
6
5
T
3
6
8
A
3
6
9
R
3
7
5
L
5
2
2
G
5
2
4
K
5
2
5
T
5
2
6
Y
5
2
9
K
5
3
3
T
5
4
4
Q
5
4
5
C
5
4
6
V
5
4
7
Q
5
4
8
N
5
5
1
Q
5
5
8
T
5
5
9
N
5
6
2
L
5
6
3
K
5
6
6
K
5
7
0
K
7
0
9
R
7
1
0
R
7
1
4
H
7
5
3
A
7
5
4
G
7
5
5
I
7
5
6
Q
7
5
7
G
7
5
8
T
7
5
9
S
7
6
0
R
7
6
1
Y
7
9
0
R
7
9
2
C
7
9
3
R
7
9
5
V
7
9
7
S
7
9
8
Y
8
0
4
L
8
0
8
F
8
1
1
R
8
1
2
Y
8
1
5
Y
8
5
7
F
8
5
8
A
8
5
9
[1]3luc.a - - - - - - - - - - . . . . . . . . . . * . . . * . * . - - - - - - - - - - - - - - - - - - - - - - - - - -
[1]3lud.a - - - - - - - - - - . . . . . . . . . . * . . . * . * . - - - - - - - - - - - - - - - - - - - - - - - - - -
[1]3lug.a - - - - - - - - - - . . . . . . . . . . * . . . * . * . - - - - - - - - - - - - - - - - - - - - - - - - - -
[1]3luh.a - - - - - - - - - - . . . . . . . . . . * . . . * . * . - - - - - - - - - - - - - - - - - - - - - - - - - -
[1]3luj.a - - - - - - - - - - . . . . . . . . . . * . . . * . * . - - - - - - - - - - - - - - - - - - - - - - - - - -
[1]3qx8.a - - - - - - - - - - . . . . . . . . . . * . . . * . * . - - - - - - - - - - - - - - - - - - - - - - - - - -
[1]3qx9.a - - - - - - - - - - . . . . . . . . . . * . . . * . * . - - - - - - - - - - - - - - - - - - - - - - - - - -
[1]4f3t.a . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . * . . . .
[1]4olb.a . . . . . . . . . . . . * . . . . . . . . . . . . . . . * . . . . . . . . . . . . . . . . . . . . * . . . .
[1]4w5n.a . . . . . . . . . . . . * . . . . . . . . . . . . . . . . . . . . . . * . . . . . . . . . . . . . * . . . .
[1]4w5r.a . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . * * . . .
[1]4w5t.a . . . . . . . . . . . . * . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . * * . . .
[1]5js1.a . . . . . . . . . . . . * . . . . . . . . . . . . . . . * . . . . . . . . . . . . . . . . . . . . * . . . .
[1]5js2.a . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . * . . . .
[1]5ki6.a . . . . . . . . . . . . . . . . . . . . * . . . . . . . . . . . . . . . . . . . . . . . . . . . . * . . . .
[1]5t7b.a . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . * . . . .
[1]5wea.a . . . - - A 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

zoom: [−] [+]; [view as image]; [download as text]

pocketligand
≥10
9
8
7
6
5
4
3
2
1
0
3luc.a is apo
3lud.a:amp
3lug.a:c5p
3luh.a:5gp
3luj.a:u5p
3qx8.a:gtg
3qx9.a:atp
4f3t.a:UAAAGU
4olb.a:AAAAAA
4w5n.a:UUCACAU
4w5r.a:UUCACA
4w5t.a:UUCACAUU
5js1.a:UUAUCU
5js2.a:6op.f2t.6nw.uft.6oo.uft
5ki6.a:6u0GGAGU
5t7b.a:uvpUAUAG
5wea.a:AAAAAAA
[1] 3luc.a
-
0.2 0.1 0.1 1.2 0.9 0 4.5 3.6 5.0 4.3 4.3 5.0 3.8 3.8 5.8 4.3
[1] 3lud.a -
0
0 0 0.6 0.5 0 4.3 3.5 3.9 4.3 4.3 4.6 3.8 4.0 5.5 4.3
[1] 3lug.a - 0.1
0
0 0.9 0.6 0.1 4.4 3.5 4.0 4.0 4.4 4.8 3.8 4.0 5.7 4.1
[1] 3luh.a - 0.1 0
0
0.8 0.7 0.1 4.2 3.2 3.8 3.9 4.2 4.8 3.9 4.4 5.5 4.0
[1] 3luj.a - 0.1 0 0
0
0.7 0 3.7 3.8 3.5 3.7 3.8 3.5 4.2 3.7 4.9 4.4
[1] 3qx8.a - 0 0 0 0.6
0.3
0.1 3.8 3.2 3.6 3.4 3.6 3.9 3.2 4.2 5.4 4.3
[1] 3qx9.a - 0.1 0 0 1.0 0.5
0
3.9 3.2 3.4 3.8 3.8 4.2 3.7 4.0 5.2 4.2
[1] 4f3t.a - 0.2 0.1 0.1 0.2 1.8 2.5
0.2
0 0.2 0.9 1.1 0.5 1.1 0.9 1.2 0.5
[1] 4olb.a - 0.1 0.2 0.2 0.4 2.2 2.7 0.4
0.1
0.5 1.2 1.0 0.8 1.8 2.1 1.6 0.3
[1] 4w5n.a - 0.2 0.1 0.1 0.3 2.1 2.9 1.7 0.2
0.5
0.3 1.0 0.7 1.2 2.5 1.8 0.6
[1] 4w5r.a - 0.2 0.2 0.1 0.2 2.7 1.9 0.3 0.4 0.4
0.3
0.5 0.4 1.9 1.7 1.6 0.7
[1] 4w5t.a - 0.4 0.2 0.2 0.3 2.6 1.9 0.5 0.4 0.4 0.2
0.1
0.2 1.7 1.8 1.2 0.2
[1] 5js1.a - 0.3 0.2 0.2 0.2 2.0 2.7 0.4 0.2 0.9 0.9 1.1
0
1.4 1.9 1.2 0.5
[1] 5js2.a - 0 0.1 0 0 2.1 2.3 0.2 0.2 0.2 0.9 0.9 0.1
0.1
0.7 0.6 0.6
[1] 5ki6.a - 0.1 0.1 0.1 0.9 1.9 2.4 0.7 0 0.5 1.3 2.1 0.9 1.4
0.3
1.7 0.4
[1] 5t7b.a - 0.1 0.1 0 0.1 1.9 2.3 0.3 0.2 0.6 1.0 1.3 0.4 0.7 1.3
0.2
0.5
[1] 5wea.a - 0.2 0.1 0.1 0.2 1.5 1.3 1.3 0.4 0.8 0.5 0.8 0.6 1.8 1.5 1.0
0.4
[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
3luc.a
3lud.a
3lug.a
3luh.a
3luj.a
3qx8.a
3qx9.a
4f3t.a
4olb.a
4w5n.a
4w5r.a
4w5t.a
5js1.a
5js2.a
5ki6.a
5t7b.a
5wea.a
[1] 3luc.a
0
.05 .03 .03 .05 .04 .03 .20 .22 .23 .21 .21 .23 .20 .19 .23 .19
[1] 3lud.a .05
0
.03 .03 .02 .02 .03 .19 .20 .21 .18 .19 .21 .19 .18 .20 .17
[1] 3lug.a .03 .03
0
.02 .03 .03 .02 .20 .21 .22 .20 .20 .22 .19 .19 .22 .18
[1] 3luh.a .03 .03 .02
0
.05 .04 .03 .21 .20 .21 .19 .19 .21 .19 .19 .21 .19
[1] 3luj.a .05 .02 .03 .05
0
.02 .03 .18 .19 .21 .18 .18 .20 .18 .17 .20 .16
[1] 3qx8.a .04 .02 .03 .04 .02
0
.02 .19 .19 .21 .19 .19 .20 .18 .19 .20 .17
[1] 3qx9.a .03 .03 .02 .03 .03 .02
0
.19 .21 .22 .20 .21 .22 .19 .19 .22 .18
[1] 4f3t.a .20 .19 .20 .21 .18 .19 .19
0
.05 .09 .08 .09 .07 .07 .05 .07 .10
[1] 4olb.a .22 .20 .21 .20 .19 .19 .21 .05
0
.07 .08 .08 .05 .11 .08 .08 .10
[1] 4w5n.a .23 .21 .22 .21 .21 .21 .22 .09 .07
0
.11 .11 .09 .11 .10 .12 .11
[1] 4w5r.a .21 .18 .20 .19 .18 .19 .20 .08 .08 .11
0
.03 .09 .11 .10 .11 .09
[1] 4w5t.a .21 .19 .20 .19 .18 .19 .21 .09 .08 .11 .03
0
.09 .10 .11 .10 .10
[1] 5js1.a .23 .21 .22 .21 .20 .20 .22 .07 .05 .09 .09 .09
0
.09 .11 .09 .11
[1] 5js2.a .20 .19 .19 .19 .18 .18 .19 .07 .11 .11 .11 .10 .09
0
.07 .07 .11
[1] 5ki6.a .19 .18 .19 .19 .17 .19 .19 .05 .08 .10 .10 .11 .11 .07
0
.08 .10
[1] 5t7b.a .23 .20 .22 .21 .20 .20 .22 .07 .08 .12 .11 .10 .09 .07 .08
0
.10
[1] 5wea.a .19 .17 .18 .19 .16 .17 .18 .10 .10 .11 .09 .10 .11 .11 .10 .10
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 1.4 Å)

Pockets (x) vs pockets (y) colored by RMSD of site residue backbone 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
3luc.a
3lud.a
3lug.a
3luh.a
3luj.a
3qx8.a
3qx9.a
4f3t.a
4olb.a
4w5n.a
4w5r.a
4w5t.a
5js1.a
5js2.a
5ki6.a
5t7b.a
5wea.a
[1] 3luc.a
0
0.3 0.1 0.1 0.4 0.3 0.2 0.9 0.8 0.8 0.8 0.8 1.0 1.0 0.8 1.0 0.8
[1] 3lud.a 0.3
0
0.2 0.2 0.2 0.2 0.3 0.9 0.8 0.9 0.8 0.8 1.0 1.0 0.8 1.0 0.9
[1] 3lug.a 0.1 0.2
0
0.1 0.3 0.2 0.2 0.8 0.8 0.8 0.7 0.7 0.9 0.9 0.8 0.9 0.8
[1] 3luh.a 0.1 0.2 0.1
0
0.3 0.2 0.2 0.8 0.8 0.8 0.7 0.7 0.9 0.9 0.8 0.9 0.8
[1] 3luj.a 0.4 0.2 0.3 0.3
0
0.3 0.4 0.8 0.8 0.8 0.8 0.7 0.9 1.0 0.8 1.0 0.9
[1] 3qx8.a 0.3 0.2 0.2 0.2 0.3
0
0.2 0.8 0.8 0.8 0.7 0.7 0.9 0.9 0.8 0.9 0.8
[1] 3qx9.a 0.2 0.3 0.2 0.2 0.4 0.2
0
0.8 0.8 0.8 0.7 0.7 0.9 0.9 0.8 0.9 0.8
[1] 4f3t.a 0.9 0.9 0.8 0.8 0.8 0.8 0.8
0
0.3 0.7 1.4 1.4 0.4 0.6 0.3 0.4 0.7
[1] 4olb.a 0.8 0.8 0.8 0.8 0.8 0.8 0.8 0.3
0
0.5 1.4 1.4 0.6 0.8 0.4 0.5 0.7
[1] 4w5n.a 0.8 0.9 0.8 0.8 0.8 0.8 0.8 0.7 0.5
0
1.1 1.2 0.8 0.9 0.7 0.8 0.9
[1] 4w5r.a 0.8 0.8 0.7 0.7 0.8 0.7 0.7 1.4 1.4 1.1
0
0.2 1.4 1.5 1.5 1.4 1.1
[1] 4w5t.a 0.8 0.8 0.7 0.7 0.7 0.7 0.7 1.4 1.4 1.2 0.2
0
1.4 1.5 1.5 1.4 1.1
[1] 5js1.a 1.0 1.0 0.9 0.9 0.9 0.9 0.9 0.4 0.6 0.8 1.4 1.4
0
0.7 0.7 0.5 0.8
[1] 5js2.a 1.0 1.0 0.9 0.9 1.0 0.9 0.9 0.6 0.8 0.9 1.5 1.5 0.7
0
0.8 0.8 1.0
[1] 5ki6.a 0.8 0.8 0.8 0.8 0.8 0.8 0.8 0.3 0.4 0.7 1.5 1.5 0.7 0.8
0
0.5 0.8
[1] 5t7b.a 1.0 1.0 0.9 0.9 1.0 0.9 0.9 0.4 0.5 0.8 1.4 1.4 0.5 0.8 0.5
0
0.7
[1] 5wea.a 0.8 0.9 0.8 0.8 0.9 0.8 0.8 0.7 0.7 0.9 1.1 1.1 0.8 1.0 0.8 0.7
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 0.8 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
3luc.a
3lud.a
3lug.a
3luh.a
3luj.a
3qx8.a
3qx9.a
4f3t.a
4olb.a
4w5n.a
4w5r.a
4w5t.a
5js1.a
5js2.a
5ki6.a
5t7b.a
5wea.a
[1] 3luc.a
0
0.7 0.8 0.7 1.1 0.5 0.7 1.4 1.4 1.5 1.4 1.4 1.6 1.8 1.5 1.8 1.6
[1] 3lud.a 0.7
0
0.4 0.5 0.8 0.6 0.9 1.4 1.4 1.6 1.4 1.4 1.6 1.8 1.6 1.8 1.6
[1] 3lug.a 0.8 0.4
0
0.5 0.8 0.7 1.0 1.5 1.5 1.6 1.4 1.4 1.6 1.8 1.6 1.8 1.7
[1] 3luh.a 0.7 0.5 0.5
0
0.9 0.5 0.8 1.4 1.4 1.5 1.3 1.3 1.6 1.8 1.5 1.7 1.6
[1] 3luj.a 1.1 0.8 0.8 0.9
0
0.9 1.2 1.4 1.6 1.6 1.5 1.5 1.7 1.8 1.8 1.8 1.7
[1] 3qx8.a 0.5 0.6 0.7 0.5 0.9
0
0.7 1.3 1.3 1.4 1.3 1.2 1.5 1.7 1.4 1.6 1.5
[1] 3qx9.a 0.7 0.9 1.0 0.8 1.2 0.7
0
1.3 1.3 1.3 1.2 1.2 1.5 1.7 1.3 1.6 1.6
[1] 4f3t.a 1.4 1.4 1.5 1.4 1.4 1.3 1.3
0
0.8 0.9 1.6 1.7 0.8 1.0 0.8 0.7 1.1
[1] 4olb.a 1.4 1.4 1.5 1.4 1.6 1.3 1.3 0.8
0
1.0 1.5 1.6 0.8 1.1 1.0 1.0 1.1
[1] 4w5n.a 1.5 1.6 1.6 1.5 1.6 1.4 1.3 0.9 1.0
0
1.5 1.6 1.1 1.3 1.0 1.2 1.2
[1] 4w5r.a 1.4 1.4 1.4 1.3 1.5 1.3 1.2 1.6 1.5 1.5
0
0.4 1.6 1.7 1.8 1.7 1.4
[1] 4w5t.a 1.4 1.4 1.4 1.3 1.5 1.2 1.2 1.7 1.6 1.6 0.4
0
1.6 1.7 1.8 1.7 1.4
[1] 5js1.a 1.6 1.6 1.6 1.6 1.7 1.5 1.5 0.8 0.8 1.1 1.6 1.6
0
0.9 1.0 0.9 1.0
[1] 5js2.a 1.8 1.8 1.8 1.8 1.8 1.7 1.7 1.0 1.1 1.3 1.7 1.7 0.9
0
1.2 1.1 1.3
[1] 5ki6.a 1.5 1.6 1.6 1.5 1.8 1.4 1.3 0.8 1.0 1.0 1.8 1.8 1.0 1.2
0
1.0 1.1
[1] 5t7b.a 1.8 1.8 1.8 1.7 1.8 1.6 1.6 0.7 1.0 1.2 1.7 1.7 0.9 1.1 1.0
0
1.1
[1] 5wea.a 1.6 1.6 1.7 1.6 1.7 1.5 1.6 1.1 1.1 1.2 1.4 1.4 1.0 1.3 1.1 1.1
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

L C X E | Background Color: | Anaglyph Stereo:

loading...