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PAFA_HUMAN_46_428

Platelet-activating factor acetylhydrolase [AB hydrolase superfamily. Lipase family]

Composition of the binding site

Protein chains monomer
A1 (PAFA_HUMAN):97, 98, 104, 107, 110, 111, 117, 121, 125, 152:155, 159, 160, 214, 272:274, 298, 322, 351, 352, 355:357, 360, 361, 369:37197, 98, 104, 107, 110, 111, 117, 121, 125, 152:155, 159, 160, 214, 272:274, 298, 322, 351, 352, 355:357, 360, 361, 369:371

Full PDB list

3d59, 3d5e, 3f96, 3f97, 3f98, 3f9c, 5i8p, 5i9i, 5jad, 5jah, 5jal, 5jan, 5jao, 5jap, 5jar, 5jas, 5jat, 5jau, 5lp1, 5lyy, 5lz2, 5lz4, 5lz5, 5lz7, 5lz8, 5lz9

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1
W
9
7
I
9
8
L
1
0
7
F
1
1
0
L
1
1
1
L
1
2
1
F
1
2
5
G
1
5
2
L
1
5
3
G
1
5
4
A
1
5
5
L
1
5
9
Y
1
6
0
E
2
1
4
H
2
7
2
S
2
7
3
F
2
7
4
W
2
9
8
F
3
2
2
H
3
5
1
Q
3
5
2
A
3
5
5
D
3
5
6
F
3
5
7
A
3
6
0
T
3
6
1
L
3
6
9
L
3
7
1
[1]3d59.a none . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]3d5e.b dep8 . . . . . . . . . . . . . . . * . . . . . . . . . . . .
[1]3f96.a none . . . . . . . . . . . . . . . * . . . . . . . . . . . .
[1]3f97.a gd710 . . . . . . . . . . . . . . . * . . . . . . . . . . . .
[1]3f98.a ntj8 . . . . . . . . . . . . . . . * . . . . . . . . . . . .
[1]3f9c.a dfp10 . . . . . . . . . . . . . . . * . . . . . . . . . . . .
[1]5i8p.a vq738 . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]5i9i.b 5hv47 . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]5jad.a fb210 . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]5jah.a 6hq10 . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]5jal.a 6ho14 . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]5jan.a 6hp15 . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]5jao.a 6hx15 . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]5jap.a 6hz21 . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]5jar.a 6hv21 . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]5jas.a 6hw20 . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]5jat.a 6hr24 . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]5jau.a 6hu30 . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]5lp1.a 71h46 . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]5lyy.a 7bj22 . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]5lz2.a 7bx15 . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]5lz4.a 7bw20 . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]5lz5.a 7k425 . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]5lz7.a 7bk25 . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]5lz8.a 7bp22 . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]5lz9.a 7br27 . . . . . . . . . . . . . . . . . . . . . . . . . . . .

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
W
9
7
I
9
8
F
1
0
4
L
1
0
7
F
1
1
0
L
1
1
1
M
1
1
7
L
1
2
1
F
1
2
5
G
1
5
2
L
1
5
3
G
1
5
4
A
1
5
5
L
1
5
9
Y
1
6
0
E
2
1
4
H
2
7
2
S
2
7
3
F
2
7
4
W
2
9
8
F
3
2
2
H
3
5
1
Q
3
5
2
A
3
5
5
D
3
5
6
F
3
5
7
A
3
6
0
T
3
6
1
L
3
6
9
K
3
7
0
L
3
7
1
[1]3d59.a . . . . . . . . . . . . . . . . . * . . . . . . . * . . . . .
[1]3d5e.b . . . . . . . . . . . . . . . . . * . . . . . . . * . . . . .
[1]3f96.a . . . . . . . . . . . . . . . . . sgb . . . . . . . * . . . . .
[1]3f97.a . . . . . . . . . . . . . . . . . * . . . . . . . * . . . . .
[1]3f98.a . . . . . . . . . . . . . . . . . * . . . . . . . * . . . . .
[1]3f9c.a . . . . . . . . . . . . . . . . . * . . . . . . . * . . . . .
[1]5i8p.a . . . . . . . . . . . . . . . . . . . . . . . . . * . . . . .
[1]5i9i.b . . . . . . . . . . . . . . . . . . . . . . . . . * . . . . .
[1]5jad.a . . . . . . . . . . . . . . . . . * . . . . . . . * . . . . .
[1]5jah.a . . . . . . . . . . . . . . . . . . . . . . . . . * . . . . .
[1]5jal.a . . . . . . . . . . . . . . . . . * . . . . . . . * . . . . .
[1]5jan.a . . . . . . . . . . . . . . . . . * . . . . . . . * . . . . .
[1]5jao.a . . . . . . . . . . . . . . . . . . . . . . . . . * . . . . .
[1]5jap.a . . . . . . . . . . . . . . . . . * . . . . . . . * . . . . .
[1]5jar.a . . . . . . . . . . . . . . . . . * . . . . . . . * . . . . .
[1]5jas.a . . . . . . . . . . . . . . . . . * . . . . . . . * . . . . .
[1]5jat.a . . . . . . . . . . . . . . . . . * . . . . . . . * . . . . .
[1]5jau.a . . . . . . . . . . . . . . . . . * . . . . . . . * . . . . .
[1]5lp1.a . . . . . . . . . . . . . . . . . . . . . . . . . * . . . . .
[1]5lyy.a . . . . . . . . . . . . . . . . . . . . . . . . . * . . . . .
[1]5lz2.a . . . . . . . . . . . . . . . . . * . . . . . . . * . . . . .
[1]5lz4.a . . . . . . . . . . . . . . . . . . . . . . . . . * . . . . .
[1]5lz5.a . . . . . . . . . . . . . . . . . . . . . . . . . * . . . . .
[1]5lz7.a . . . . . . . . . . . . . . . . . . . . . . . . . * . . . . .
[1]5lz8.a . . . . . . . . . . . . . . . . . . . . . . . . . * . . . . .
[1]5lz9.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
3d59.a is apo
3d5e.b:dep
3f96.a is apo
3f97.a:gd7
3f98.a:ntj
3f9c.a:dfp
5i8p.a:vq7
5i9i.b:5hv
5jad.a:fb2
5jah.a:6hq
5jal.a:6ho
5jan.a:6hp
5jao.a:6hx
5jap.a:6hz
5jar.a:6hv
5jas.a:6hw
5jat.a:6hr
5jau.a:6hu
5lp1.a:71h
5lyy.a:7bj
5lz2.a:7bx
5lz4.a:7bw
5lz5.a:7k4
5lz7.a:7bk
5lz8.a:7bp
5lz9.a:7br
[1] 3d59.a
-
0.5 - 0.5 0.9 0.7 0.2 0.2 0 0.2 0 0 1.2 1.1 1.2 1.1 1.3 1.3 0.1 0.2 0.1 0.2 0.2 0.2 0.2 0.2
[1] 3d5e.b -
0.4
- 0.5 0.4 0.5 0.2 0.1 0 0.1 0 0.1 1.4 1.2 1.2 1.3 1.3 1.3 0.1 0.2 0 0.2 0.2 0.2 0.2 0.2
[1] 3f96.a - 5.4
-
5.2 5.3 5.4 4.6 4.6 1.8 4.8 0 1.0 1.3 1.3 1.5 1.3 2.2 2.5 4.6 4.6 2.3 4.7 4.4 4.7 4.8 4.5
[1] 3f97.a - 0.5 -
0.6
0.8 0.9 0.2 0.1 0 0.2 0 0 1.4 1.3 1.4 1.3 1.4 1.3 0.1 0.2 0.1 0.2 0.2 0.2 0.2 0.2
[1] 3f98.a - 0.4 - 0.7
0.4
0.5 0.3 0.4 0.1 0.2 0 0.1 1.6 1.6 1.3 1.3 1.3 1.4 0.3 0.3 0.2 0.2 0.2 0.2 0.3 0.2
[1] 3f9c.a - 0.5 - 0.5 0.6
0.5
0.3 0.2 0.1 0.1 0 0.3 1.4 1.3 1.4 1.3 1.4 1.2 0.1 0.1 0.1 0.1 0.1 0.2 0.1 0.2
[1] 5i8p.a - 0.4 - 0.5 0.4 0.5
0.1
0.2 0.1 0 0 0.2 1.4 1.2 1.2 1.3 1.3 1.3 0.2 0.2 0.1 0.2 0.1 0.2 0.2 0.2
[1] 5i9i.b - 0.5 - 0.5 0.4 0.5 0.2
0
0 0 0.1 0 1.9 1.6 1.5 1.6 1.5 1.6 0.1 0 0 0.2 0.1 0.2 0.2 0.2
[1] 5jad.a - 0.4 - 0.7 0.6 0.7 0.3 0.3
0
0.1 0 0 1.4 1.4 1.4 1.4 1.6 1.5 0.1 0.2 0 0.2 0.1 0.2 0.2 0.2
[1] 5jah.a - 0.4 - 0.6 0.6 0.4 0.3 0.2 0.3
0.1
0 0.1 1.3 1.5 1.5 1.4 1.6 1.6 0.3 0.1 0.2 0.1 0.1 0.2 0.2 0.2
[1] 5jal.a - 0.4 - 0.8 0.8 0.7 0.4 0.4 0.3 0.1
0
0.1 1.2 1.1 1.2 1.1 1.3 1.4 0.3 0.2 0.3 0.3 0.2 0.3 0.3 0.3
[1] 5jan.a - 0.4 - 0.8 0.8 0.9 0.2 0.1 0.1 0.1 0
0
1.2 1.2 1.2 1.1 1.5 1.4 0.1 0.1 0.2 0.1 0.2 0.2 0.1 0.3
[1] 5jao.a - 0.4 - 0.6 0.6 0.7 1.9 1.6 1.1 0.1 0.2 0.1
0
0.5 0.2 0.2 0.1 0.3 1.5 0.9 1.3 1.4 1.4 1.2 1.4 1.4
[1] 5jap.a - 0.5 - 1.4 0.8 1.0 1.9 2.1 1.4 0.1 0 0.1 0
0
0 0 0.1 0.3 1.7 1.0 1.6 1.8 1.7 1.8 1.7 1.7
[1] 5jar.a - 0.5 - 1.1 0.8 0.6 1.9 1.9 1.4 0.1 0 0.1 0 0
0
0 0.1 0.3 1.7 1.1 1.8 1.6 1.6 1.7 1.6 1.7
[1] 5jas.a - 0.5 - 1.0 0.6 0.6 1.9 1.9 1.3 0.1 0 0.1 0 0.1 0
0
0.1 0.3 1.7 0.9 1.9 1.6 1.6 1.7 1.7 1.7
[1] 5jat.a - 0.4 - 0.7 0.8 0.9 1.4 1.1 0.5 0.1 0.3 0.1 0.1 0.4 0.4 0.1
0
0 1.1 0.8 0.8 1.0 0.9 0.9 1.0 1.0
[1] 5jau.a - 0.4 - 0.5 0.6 0.5 1.4 1.2 0.6 0.1 0 0.1 0.1 0 0 0 0
0
1.1 0.8 0.8 1.0 1.1 1.0 1.2 1.2
[1] 5lp1.a - 0.4 - 0.5 0.4 0.5 0.2 0 0 0 0 0.1 1.4 1.4 1.4 1.3 1.5 1.5
0
0 0 0 0.2 0.1 0 0.1
[1] 5lyy.a - 0.4 - 0.6 0.4 0.5 0.2 0.4 0 0.1 0 0.6 1.4 1.4 1.4 1.4 1.4 1.6 0.1
0.1
0 0.1 0.1 0.2 0.1 0.2
[1] 5lz2.a - 0.4 - 0.6 0.8 0.9 0.2 0.2 0 0.1 0 0 2.0 1.8 1.9 1.8 1.6 1.4 0.1 0.2
0
0.2 0.1 0.2 0.2 0.2
[1] 5lz4.a - 0.4 - 0.6 0.4 0.4 0.1 0.3 0.1 0 0 0.1 1.9 1.7 1.9 1.8 1.5 1.5 0.1 0 0
0.1
0.1 0 0.1 0.1
[1] 5lz5.a - 0.4 - 0.6 0.4 0.4 0.2 0.3 0.1 0 0 0 2.0 1.8 1.9 1.8 1.6 1.7 0.1 0 0.1 0
0.1
0 0 0
[1] 5lz7.a - 0.4 - 0.5 0.4 0.4 0.2 0.1 0.1 0 0 0.3 1.9 1.8 1.9 2.0 1.6 1.5 0 0 0 0 0.1
0
0 0.1
[1] 5lz8.a - 0.5 - 0.7 0.4 0.4 0 0.1 0.1 0 0 0.3 1.7 1.6 1.5 1.6 1.5 1.4 0.1 0 0.1 0 0.1 0
0
0
[1] 5lz9.a - 0.4 - 0.6 0.4 0.4 0.1 0.2 0.1 0 0 0.5 1.9 1.6 1.7 1.9 1.5 1.4 0.1 0 0.1 0 0.1 0 0
0
[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
3d59.a
3d5e.b
3f96.a
3f97.a
3f98.a
3f9c.a
5i8p.a
5i9i.b
5jad.a
5jah.a
5jal.a
5jan.a
5jao.a
5jap.a
5jar.a
5jas.a
5jat.a
5jau.a
5lp1.a
5lyy.a
5lz2.a
5lz4.a
5lz5.a
5lz7.a
5lz8.a
5lz9.a
[1] 3d59.a
0
.02 .16 .01 .04 .04 .02 .05 .03 .02 .02 .01 .05 .05 .04 .06 .02 .02 .03 .05 .04 .05 .05 .05 .06 .06
[1] 3d5e.b .02
0
.17 .03 .03 .03 .01 .04 .03 .03 .03 .03 .04 .06 .05 .05 .03 .02 .02 .03 .05 .04 .04 .03 .04 .04
[1] 3f96.a .16 .17
0
.15 .19 .18 .18 .19 .17 .17 .18 .16 .20 .21 .20 .21 .18 .18 .17 .18 .18 .20 .19 .19 .20 .21
[1] 3f97.a .01 .03 .15
0
.05 .03 .03 .05 .02 .03 .03 .02 .06 .06 .05 .07 .03 .03 .03 .05 .03 .06 .05 .05 .06 .07
[1] 3f98.a .04 .03 .19 .05
0
.06 .03 .04 .05 .04 .05 .04 .05 .07 .06 .06 .06 .04 .03 .05 .06 .05 .05 .04 .05 .05
[1] 3f9c.a .04 .03 .18 .03 .06
0
.03 .06 .04 .04 .04 .05 .06 .08 .07 .07 .05 .04 .04 .03 .06 .05 .06 .04 .05 .06
[1] 5i8p.a .02 .01 .18 .03 .03 .03
0
.05 .04 .03 .03 .03 .05 .07 .06 .06 .04 .03 .03 .03 .06 .04 .05 .03 .04 .04
[1] 5i9i.b .05 .04 .19 .05 .04 .06 .05
0
.05 .05 .06 .05 .05 .08 .07 .06 .07 .06 .04 .05 .04 .04 .02 .03 .03 .04
[1] 5jad.a .03 .03 .17 .02 .05 .04 .04 .05
0
.02 .03 .02 .04 .07 .06 .05 .04 .03 .02 .03 .04 .05 .05 .05 .05 .05
[1] 5jah.a .02 .03 .17 .03 .04 .04 .03 .05 .02
0
.03 .02 .04 .06 .05 .05 .03 .03 .02 .03 .05 .05 .06 .04 .05 .06
[1] 5jal.a .02 .03 .18 .03 .05 .04 .03 .06 .03 .03
0
.03 .03 .03 .03 .04 .02 .03 .04 .05 .05 .05 .06 .06 .07 .06
[1] 5jan.a .01 .03 .16 .02 .04 .05 .03 .05 .02 .02 .03
0
.05 .06 .05 .06 .03 .03 .03 .04 .04 .06 .06 .05 .05 .05
[1] 5jao.a .05 .04 .20 .06 .05 .06 .05 .05 .04 .04 .03 .05
0
.02 .02 .01 .02 .03 .05 .06 .06 .05 .06 .05 .06 .05
[1] 5jap.a .05 .06 .21 .06 .07 .08 .07 .08 .07 .06 .03 .06 .02
0
.01 .02 .03 .04 .07 .07 .06 .06 .07 .08 .08 .07
[1] 5jar.a .04 .05 .20 .05 .06 .07 .06 .07 .06 .05 .03 .05 .02 .01
0
.02 .02 .05 .06 .07 .06 .06 .07 .07 .07 .07
[1] 5jas.a .06 .05 .21 .07 .06 .07 .06 .06 .05 .05 .04 .06 .01 .02 .02
0
.03 .03 .06 .06 .06 .05 .06 .06 .06 .05
[1] 5jat.a .02 .03 .18 .03 .06 .05 .04 .07 .04 .03 .02 .03 .02 .03 .02 .03
0
.03 .04 .06 .06 .06 .07 .07 .07 .07
[1] 5jau.a .02 .02 .18 .03 .04 .04 .03 .06 .03 .03 .03 .03 .03 .04 .05 .03 .03
0
.03 .03 .06 .05 .05 .05 .06 .05
[1] 5lp1.a .03 .02 .17 .03 .03 .04 .03 .04 .02 .02 .04 .03 .05 .07 .06 .06 .04 .03
0
.03 .05 .04 .05 .03 .04 .05
[1] 5lyy.a .05 .03 .18 .05 .05 .03 .03 .05 .03 .03 .05 .04 .06 .07 .07 .06 .06 .03 .03
0
.06 .04 .05 .03 .04 .03
[1] 5lz2.a .04 .05 .18 .03 .06 .06 .06 .04 .04 .05 .05 .04 .06 .06 .06 .06 .06 .06 .05 .06
0
.03 .03 .04 .06 .04
[1] 5lz4.a .05 .04 .20 .06 .05 .05 .04 .04 .05 .05 .05 .06 .05 .06 .06 .05 .06 .05 .04 .04 .03
0
.02 .03 .04 .03
[1] 5lz5.a .05 .04 .19 .05 .05 .06 .05 .02 .05 .06 .06 .06 .06 .07 .07 .06 .07 .05 .05 .05 .03 .02
0
.03 .04 .03
[1] 5lz7.a .05 .03 .19 .05 .04 .04 .03 .03 .05 .04 .06 .05 .05 .08 .07 .06 .07 .05 .03 .03 .04 .03 .03
0
.02 .02
[1] 5lz8.a .06 .04 .20 .06 .05 .05 .04 .03 .05 .05 .07 .05 .06 .08 .07 .06 .07 .06 .04 .04 .06 .04 .04 .02
0
.03
[1] 5lz9.a .06 .04 .21 .07 .05 .06 .04 .04 .05 .06 .06 .05 .05 .07 .07 .05 .07 .05 .05 .03 .04 .03 .03 .02 .03
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 0.6 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
3d59.a
3d5e.b
3f96.a
3f97.a
3f98.a
3f9c.a
5i8p.a
5i9i.b
5jad.a
5jah.a
5jal.a
5jan.a
5jao.a
5jap.a
5jar.a
5jas.a
5jat.a
5jau.a
5lp1.a
5lyy.a
5lz2.a
5lz4.a
5lz5.a
5lz7.a
5lz8.a
5lz9.a
[1] 3d59.a
0
0.2 0.3 0.1 0.3 0.2 0.2 0.4 0.2 0.3 0.3 0.2 0.3 0.4 0.4 0.3 0.3 0.3 0.3 0.3 0.3 0.3 0.3 0.3 0.3 0.3
[1] 3d5e.b 0.2
0
0.3 0.2 0.3 0.3 0.3 0.4 0.3 0.4 0.4 0.2 0.4 0.5 0.4 0.4 0.4 0.4 0.4 0.4 0.4 0.4 0.4 0.4 0.4 0.4
[1] 3f96.a 0.3 0.3
0
0.3 0.3 0.3 0.3 0.3 0.2 0.3 0.4 0.2 0.4 0.4 0.4 0.4 0.4 0.4 0.3 0.3 0.3 0.3 0.3 0.3 0.3 0.3
[1] 3f97.a 0.1 0.2 0.3
0
0.3 0.2 0.2 0.4 0.2 0.3 0.3 0.2 0.3 0.4 0.3 0.3 0.3 0.3 0.3 0.3 0.3 0.3 0.3 0.3 0.3 0.3
[1] 3f98.a 0.3 0.3 0.3 0.3
0
0.3 0.3 0.3 0.3 0.3 0.3 0.2 0.3 0.3 0.3 0.3 0.3 0.3 0.3 0.3 0.3 0.3 0.3 0.3 0.3 0.3
[1] 3f9c.a 0.2 0.3 0.3 0.2 0.3
0
0.2 0.4 0.2 0.3 0.3 0.2 0.3 0.4 0.3 0.3 0.4 0.3 0.3 0.3 0.3 0.3 0.3 0.3 0.3 0.3
[1] 5i8p.a 0.2 0.3 0.3 0.2 0.3 0.2
0
0.3 0.3 0.3 0.3 0.2 0.3 0.4 0.3 0.3 0.3 0.3 0.3 0.3 0.4 0.3 0.3 0.3 0.3 0.3
[1] 5i9i.b 0.4 0.4 0.3 0.4 0.3 0.4 0.3
0
0.4 0.3 0.4 0.4 0.3 0.4 0.4 0.3 0.3 0.3 0.3 0.3 0.4 0.4 0.3 0.3 0.3 0.4
[1] 5jad.a 0.2 0.3 0.2 0.2 0.3 0.2 0.3 0.4
0
0.3 0.3 0.2 0.4 0.4 0.4 0.4 0.4 0.3 0.3 0.3 0.3 0.3 0.2 0.3 0.3 0.3
[1] 5jah.a 0.3 0.4 0.3 0.3 0.3 0.3 0.3 0.3 0.3
0
0.1 0.3 0.2 0.2 0.2 0.2 0.3 0.2 0.2 0.1 0.2 0.1 0.2 0.1 0.2 0.2
[1] 5jal.a 0.3 0.4 0.4 0.3 0.3 0.3 0.3 0.4 0.3 0.1
0
0.3 0.1 0.2 0.1 0.1 0.2 0.2 0.2 0.2 0.2 0.2 0.3 0.2 0.3 0.2
[1] 5jan.a 0.2 0.2 0.2 0.2 0.2 0.2 0.2 0.4 0.2 0.3 0.3
0
0.3 0.4 0.3 0.3 0.3 0.3 0.3 0.3 0.3 0.3 0.3 0.3 0.2 0.3
[1] 5jao.a 0.3 0.4 0.4 0.3 0.3 0.3 0.3 0.3 0.4 0.2 0.1 0.3
0
0.2 0.1 0.1 0.2 0.2 0.2 0.3 0.3 0.2 0.3 0.2 0.3 0.2
[1] 5jap.a 0.4 0.5 0.4 0.4 0.3 0.4 0.4 0.4 0.4 0.2 0.2 0.4 0.2
0
0.2 0.2 0.2 0.2 0.3 0.3 0.3 0.3 0.3 0.3 0.3 0.3
[1] 5jar.a 0.4 0.4 0.4 0.3 0.3 0.3 0.3 0.4 0.4 0.2 0.1 0.3 0.1 0.2
0
0.1 0.2 0.2 0.3 0.3 0.3 0.2 0.3 0.2 0.3 0.2
[1] 5jas.a 0.3 0.4 0.4 0.3 0.3 0.3 0.3 0.3 0.4 0.2 0.1 0.3 0.1 0.2 0.1
0
0.2 0.2 0.2 0.2 0.3 0.2 0.3 0.2 0.3 0.2
[1] 5jat.a 0.3 0.4 0.4 0.3 0.3 0.4 0.3 0.3 0.4 0.3 0.2 0.3 0.2 0.2 0.2 0.2
0
0.2 0.3 0.3 0.3 0.3 0.4 0.3 0.4 0.3
[1] 5jau.a 0.3 0.4 0.4 0.3 0.3 0.3 0.3 0.3 0.3 0.2 0.2 0.3 0.2 0.2 0.2 0.2 0.2
0
0.2 0.2 0.2 0.2 0.3 0.2 0.3 0.3
[1] 5lp1.a 0.3 0.4 0.3 0.3 0.3 0.3 0.3 0.3 0.3 0.2 0.2 0.3 0.2 0.3 0.3 0.2 0.3 0.2
0
0.2 0.2 0.2 0.2 0.2 0.2 0.2
[1] 5lyy.a 0.3 0.4 0.3 0.3 0.3 0.3 0.3 0.3 0.3 0.1 0.2 0.3 0.3 0.3 0.3 0.2 0.3 0.2 0.2
0
0.1 0.1 0.2 0.2 0.2 0.2
[1] 5lz2.a 0.3 0.4 0.3 0.3 0.3 0.3 0.4 0.4 0.3 0.2 0.2 0.3 0.3 0.3 0.3 0.3 0.3 0.2 0.2 0.1
0
0.1 0.2 0.2 0.2 0.2
[1] 5lz4.a 0.3 0.4 0.3 0.3 0.3 0.3 0.3 0.4 0.3 0.1 0.2 0.3 0.2 0.3 0.2 0.2 0.3 0.2 0.2 0.1 0.1
0
0.2 0.1 0.2 0.1
[1] 5lz5.a 0.3 0.4 0.3 0.3 0.3 0.3 0.3 0.3 0.2 0.2 0.3 0.3 0.3 0.3 0.3 0.3 0.4 0.3 0.2 0.2 0.2 0.2
0
0.2 0.2 0.2
[1] 5lz7.a 0.3 0.4 0.3 0.3 0.3 0.3 0.3 0.3 0.3 0.1 0.2 0.3 0.2 0.3 0.2 0.2 0.3 0.2 0.2 0.2 0.2 0.1 0.2
0
0.2 0.2
[1] 5lz8.a 0.3 0.4 0.3 0.3 0.3 0.3 0.3 0.3 0.3 0.2 0.3 0.2 0.3 0.3 0.3 0.3 0.4 0.3 0.2 0.2 0.2 0.2 0.2 0.2
0
0.2
[1] 5lz9.a 0.3 0.4 0.3 0.3 0.3 0.3 0.3 0.4 0.3 0.2 0.2 0.3 0.2 0.3 0.2 0.2 0.3 0.3 0.2 0.2 0.2 0.1 0.2 0.2 0.2
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 0.3 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
3d59.a
3d5e.b
3f96.a
3f97.a
3f98.a
3f9c.a
5i8p.a
5i9i.b
5jad.a
5jah.a
5jal.a
5jan.a
5jao.a
5jap.a
5jar.a
5jas.a
5jat.a
5jau.a
5lp1.a
5lyy.a
5lz2.a
5lz4.a
5lz5.a
5lz7.a
5lz8.a
5lz9.a
[1] 3d59.a
0
0.4 0.4 0.1 0.6 0.2 0.4 0.6 0.7 0.8 0.8 0.6 0.9 0.8 0.9 0.9 0.8 0.8 0.6 0.8 0.8 0.7 0.7 0.8 0.7 0.8
[1] 3d5e.b 0.4
0
0.5 0.4 0.6 0.5 0.4 0.6 0.8 0.8 0.8 0.6 0.9 0.9 0.9 0.9 0.9 0.8 0.7 0.8 0.8 0.8 0.7 0.8 0.7 0.8
[1] 3f96.a 0.4 0.5
0
0.5 0.6 0.4 0.4 0.5 0.6 0.7 0.8 0.6 0.9 0.9 0.9 0.9 0.8 0.8 0.6 0.7 0.7 0.7 0.6 0.7 0.6 0.8
[1] 3f97.a 0.1 0.4 0.5
0
0.6 0.2 0.4 0.6 0.7 0.8 0.8 0.6 0.9 0.8 0.9 0.9 0.8 0.8 0.6 0.8 0.8 0.7 0.7 0.8 0.7 0.8
[1] 3f98.a 0.6 0.6 0.6 0.6
0
0.6 0.6 0.7 0.8 0.9 0.9 0.8 1.0 0.9 1.0 1.0 0.9 0.9 0.8 0.9 0.9 0.8 0.8 0.9 0.8 0.9
[1] 3f9c.a 0.2 0.5 0.4 0.2 0.6
0
0.4 0.6 0.7 0.8 0.8 0.6 0.9 0.8 0.9 0.9 0.8 0.8 0.6 0.7 0.8 0.7 0.7 0.8 0.7 0.8
[1] 5i8p.a 0.4 0.4 0.4 0.4 0.6 0.4
0
0.6 0.6 0.6 0.7 0.4 0.8 0.8 0.8 0.8 0.7 0.7 0.6 0.6 0.6 0.6 0.5 0.6 0.5 0.7
[1] 5i9i.b 0.6 0.6 0.5 0.6 0.7 0.6 0.6
0
0.5 0.6 0.6 0.5 0.7 0.7 0.8 0.7 0.6 0.6 0.5 0.5 0.6 0.6 0.5 0.6 0.5 0.6
[1] 5jad.a 0.7 0.8 0.6 0.7 0.8 0.7 0.6 0.5
0
0.5 0.5 0.5 0.8 0.7 0.8 0.7 0.7 0.6 0.7 0.5 0.5 0.6 0.6 0.6 0.5 0.5
[1] 5jah.a 0.8 0.8 0.7 0.8 0.9 0.8 0.6 0.6 0.5
0
0.3 0.5 0.6 0.6 0.6 0.6 0.7 0.5 0.7 0.3 0.3 0.5 0.5 0.3 0.5 0.4
[1] 5jal.a 0.8 0.8 0.8 0.8 0.9 0.8 0.7 0.6 0.5 0.3
0
0.6 0.5 0.5 0.5 0.5 0.7 0.4 0.7 0.4 0.3 0.4 0.6 0.3 0.5 0.4
[1] 5jan.a 0.6 0.6 0.6 0.6 0.8 0.6 0.4 0.5 0.5 0.5 0.6
0
0.7 0.7 0.8 0.8 0.8 0.7 0.6 0.5 0.5 0.6 0.4 0.5 0.4 0.6
[1] 5jao.a 0.9 0.9 0.9 0.9 1.0 0.9 0.8 0.7 0.8 0.6 0.5 0.7
0
0.5 0.3 0.3 0.7 0.4 0.8 0.6 0.6 0.6 0.8 0.6 0.7 0.7
[1] 5jap.a 0.8 0.9 0.9 0.8 0.9 0.8 0.8 0.7 0.7 0.6 0.5 0.7 0.5
0
0.4 0.3 0.7 0.4 0.8 0.6 0.7 0.7 0.8 0.7 0.8 0.7
[1] 5jar.a 0.9 0.9 0.9 0.9 1.0 0.9 0.8 0.8 0.8 0.6 0.5 0.8 0.3 0.4
0
0.3 0.7 0.4 0.8 0.6 0.6 0.6 0.8 0.6 0.8 0.7
[1] 5jas.a 0.9 0.9 0.9 0.9 1.0 0.9 0.8 0.7 0.7 0.6 0.5 0.8 0.3 0.3 0.3
0
0.7 0.3 0.8 0.6 0.6 0.7 0.8 0.6 0.8 0.7
[1] 5jat.a 0.8 0.9 0.8 0.8 0.9 0.8 0.7 0.6 0.7 0.7 0.7 0.8 0.7 0.7 0.7 0.7
0
0.6 0.7 0.7 0.8 0.7 0.8 0.7 0.8 0.8
[1] 5jau.a 0.8 0.8 0.8 0.8 0.9 0.8 0.7 0.6 0.6 0.5 0.4 0.7 0.4 0.4 0.4 0.3 0.6
0
0.7 0.5 0.5 0.6 0.7 0.5 0.7 0.6
[1] 5lp1.a 0.6 0.7 0.6 0.6 0.8 0.6 0.6 0.5 0.7 0.7 0.7 0.6 0.8 0.8 0.8 0.8 0.7 0.7
0
0.6 0.7 0.6 0.6 0.6 0.6 0.6
[1] 5lyy.a 0.8 0.8 0.7 0.8 0.9 0.7 0.6 0.5 0.5 0.3 0.4 0.5 0.6 0.6 0.6 0.6 0.7 0.5 0.6
0
0.3 0.4 0.4 0.2 0.4 0.4
[1] 5lz2.a 0.8 0.8 0.7 0.8 0.9 0.8 0.6 0.6 0.5 0.3 0.3 0.5 0.6 0.7 0.6 0.6 0.8 0.5 0.7 0.3
0
0.4 0.5 0.3 0.5 0.4
[1] 5lz4.a 0.7 0.8 0.7 0.7 0.8 0.7 0.6 0.6 0.6 0.5 0.4 0.6 0.6 0.7 0.6 0.7 0.7 0.6 0.6 0.4 0.4
0
0.6 0.3 0.5 0.5
[1] 5lz5.a 0.7 0.7 0.6 0.7 0.8 0.7 0.5 0.5 0.6 0.5 0.6 0.4 0.8 0.8 0.8 0.8 0.8 0.7 0.6 0.4 0.5 0.6
0
0.5 0.3 0.5
[1] 5lz7.a 0.8 0.8 0.7 0.8 0.9 0.8 0.6 0.6 0.6 0.3 0.3 0.5 0.6 0.7 0.6 0.6 0.7 0.5 0.6 0.2 0.3 0.3 0.5
0
0.4 0.4
[1] 5lz8.a 0.7 0.7 0.6 0.7 0.8 0.7 0.5 0.5 0.5 0.5 0.5 0.4 0.7 0.8 0.8 0.8 0.8 0.7 0.6 0.4 0.5 0.5 0.3 0.4
0
0.5
[1] 5lz9.a 0.8 0.8 0.8 0.8 0.9 0.8 0.7 0.6 0.5 0.4 0.4 0.6 0.7 0.7 0.7 0.7 0.8 0.6 0.6 0.4 0.4 0.5 0.5 0.4 0.5
0
[Binding site full-atom RMSD matrix]







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