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SYY_METJA_1_306

Tyrosine--tRNA ligase [Class-I aminoacyl-tRNA synthetase family. TyrS type 3 subfamily]

Composition of the binding site

Protein chains monomer [domain annotation]
A1 (SYY_METJA):R: Tyrosine (151, 154, 155, 158)
32:36, 63:67, 69, 70, 72:75, 105, 108, 109, 114, 137, 147, 148, 150, 159:162, 164, 167, 172, 173
32:36, 63:67, 69, 70, 72:75, 105, 108, 109, 114, 137, 147, 148, 150, 151, 154, 155, 158:162, 164, 167, 172, 173

Full PDB list

1j1u, 1u7d, 1u7x, 1zh0, 1zh6, 2ag6, 2hgz, 2pxh, 2zp1, 3d6u, 3d6v, 3n2y, 3qe4, 4hjr, 4hjx, 4hk4, 4hpw, 4nd6, 4nd7, 4nda, 4nx2, 4pbr, 4pbs, 4pbt, 5l7p, 5n5u, 5n5v, 5u36

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1
Y
3
2
I
3
3
G
3
4
F
3
5
E
3
6
I
6
3
L
6
5
A
6
7
L
6
9
H
7
0
L
7
3
N
7
4
G
1
0
5
F
1
0
8
Q
1
0
9
I
1
3
7
A
1
4
7
I
1
5
0
Y
1
5
1
M
1
5
4
Q
1
5
5
D
1
5
8
I
1
5
9
H
1
6
0
Y
1
6
1
L
1
6
2
V
1
6
4
Q
1
7
3
[1]1j1u.a Y13 . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]1zh0.a nal16 L . . . . . . . . . . . . . . . . . . . . P A . . Q . .
[1]1zh6.a 4af15 L . . . . . . . . . . . . . . . . . . . . G C . . R . .
[1]2ag6.a 4bf13 L . . . . . . . . . . . . . . . . . . . . P L . . E . .
[1]2hgz.a pbf20 G . . . . . . . . . . . . . . . . . . . . T S . R . . .
[1]2zp1.a iyr14 . . . . . . . . . A . . . . . . . . . . . T S . . . . .
[1]3d6u.a t1119 I . . . . . . . . F . . . . M . . . . . . P L . . E . .
[1]3d6v.a tfq17 I . . . . . . . . F . . . . M . . . . . . P L . . E . .
[1]3n2y.a tef17 L . . . . . I . . . . . . . M . . . . . . G . . . V G .
[1]3qe4.b 4cf14 L . . . . . V . . . . . . W M . . . . . . G A . . . . .
[1]4hjr.a none R . . . . . Y . . G . . . N C . . . . . . N . . . S . .
[1]4hjx.a f2y15 R . . . . . Y . . G . . . N C . . . . . . N . . . S . .
[1]4hk4.a none E . . . . . S . . G . . . . G . . . . . . N . . . V . .
[1]4hpw.a 3ym15 E . . . . . S . . G . . . . G . . . . . . N . . . V . .
[1]4nd7.a none H . . . . . . . . C . . . . . . . . . . . S A . . R . .
[1]4nda.a niy16 H . . . . . . . . C . . . . . . . . . . . S A . . R . .
[1]4nx2.a 2lt15 L . . . . . I . . G . . . I L . . . . . . S . . . M . .
[1]4pbr.a 2l719 G . . . . . E . . . . . . W M . . . . . . S . . . K . .
[1]4pbs.a 2l719 G . . . . . E . . . . . . . . . . . . . . G C . . . . .
[1]4pbt.a 2lq23 G . . . . . E . . . . . . W M . . . . . . S . . . K . .
[1]5n5u.a 7n815 S . . . . . A . . M . . . . . . . . . . . S . . . E . .
[1]5n5v.a none S . . . . . A . . M . . . . . . . . . . . S . . . E . .
[2]1u7d.a none . . . . . . . . . . . . . . . - . . . . . . . . . . . .
[2]1u7x.a none Q . . . . . . . . . . . . . . . . . . . . A . . . P . .
[2]4nd6.a none H . . . . . . . . C . . . . . . . . . . . S A . . R . .
[3]5l7p.a 1pe16 A . . . . . I . . A . . . . A . . . . . . A A . . M . .
[3]5l7p.b buu24 A . . . . . I . . A . . . . A . . . . . . A A . . M . .
[4]2pxh.a bp518 G . . . . . Y . . A . . . . . . . . . . E G W . . S . .
[5]5u36.b none S . . . . . A . . . - - . - - . . . . . . G . . . K . .

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
Y
3
2
I
3
3
G
3
4
F
3
5
E
3
6
I
6
3
I
6
4
L
6
5
L
6
6
A
6
7
L
6
9
H
7
0
Y
7
2
L
7
3
N
7
4
Q
7
5
G
1
0
5
F
1
0
8
Q
1
0
9
Y
1
1
4
I
1
3
7
A
1
4
7
E
1
4
8
I
1
5
0
Y
1
5
1
M
1
5
4
Q
1
5
5
D
1
5
8
I
1
5
9
H
1
6
0
Y
1
6
1
L
1
6
2
V
1
6
4
A
1
6
7
E
1
7
2
Q
1
7
3
[1]1j1u.a * . . . . . . * . . . * . * * . . . * . . . . . . . . * . . . * . . . .
[1]1zh0.a L . . . . . . * . . . * . * * . . . * . . . . . . . . P A * . Q . V . .
[1]1zh6.a L . . . . . . * . . . * . * * . . . * . . . . . . . . G C . . R . . . .
[1]2ag6.a L . . . . . . * . . . * . * * . . . * . . . . . . . . P L * . E . . . .
[1]2hgz.a G . . . . . . . . . . * . * * . . . * . . . . . . * . T S . R * . . . .
[1]2zp1.a * . . . . . . * . . . A . * * . . . * . . . . . . . . T S . . * . . . .
[1]3d6u.a I . . . . . . . . . . F . * * . . . M . . . . . . . . P L * . E . . . .
[1]3d6v.a I . . . . . . . . . . F . * * . . . M . . . . . . . . P L * . E . . . .
[1]3n2y.a L . . . . . . I . . . * . * * . . . M . . . . . . . . G . . . V G . . .
[1]3qe4.b L . . . . . . V . . . * . * * . . W M . . * . . . . . G A . . * . . . .
[1]4hjr.a R . . . . . . Y . . . G . * * . . N C . . * . . . . . N . . . S . . . .
[1]4hjx.a R . . . . . . Y . . . G . * * . . N C . . . . . . . . N . . . S . . . .
[1]4hk4.a E . . . . . . S . . . G . * * . . . G . . . . . . * * N . . . V . . . .
[1]4hpw.a E . . . . . . S . . . G . * * . . . G . . . . . . * . N . . . V . . . .
[1]4nd7.a H . . . . . . . . . . C . * * . . . * . . . . . . . . S A . . R . . . .
[1]4nda.a H . . . . . . * . . . C . * * . . . * . . . . . . . . S A . . R . . . .
[1]4nx2.a L . . . . . . I . . . G . * . . . I L G . . . . . . . S . . . M . . . .
[1]4pbr.a G . . . . . . E . . . * . * * . . W M . . . . . . . . S . . . K . . . .
[1]4pbs.a G . . . . . . E . . . * . * * . . . * . . . . . . . . G C . . * . . . .
[1]4pbt.a G . . . . . . E . . . * . * * . . W M . . . . . . . . S . . . K . . . .
[1]5n5u.a S . . . . . . A . . . M . * * . . . * . . . . . . . . S . . . E . . . .
[1]5n5v.a S . . . . . . A . . . M . * * . . . * . . . . . . . . S . . . E . . . .
[2]1u7d.a * . . . . . . * . . . * . . . . . . * . - . . . . . . * . . . * . . . .
[2]1u7x.a Q . . . . . . * . . . . . . . . . . * . . . . . . . * A . . . P . . . .
[2]4nd6.a H . . . . . . * . . . C . . . N . . * . . . . . . . * S A . . R . . . .
[3]5l7p.a A . . . . . . I . . . A . . . . . . A . . . . . . . . A A . . M . N . .
[3]5l7p.b A . . . . . . I . . . A . * * . . . A . . . . . . . . A A . . M . N . .
[4]2pxh.a G . . . . . . Y . . . A . * * . . . * . . . . . . . E G W . . S . . . .
[5]5u36.b S . . . . . . A . . * . . - - - . - - . . . . . . . . G . * . K . . . .

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
1j1u.a:Y
1zh0.a:nal
1zh6.a:4af
2ag6.a:4bf
2hgz.a:pbf
2zp1.a:iyr
3d6u.a:t11
3d6v.a:tfq
3n2y.a:tef
3qe4.b:4cf
4hjr.a is apo
4hjx.a:f2y
4hk4.a is apo
4hpw.a:3ym
4nd7.a is apo
4nda.a:niy
4nx2.a:2lt
4pbr.a:2l7
4pbs.a:2l7
4pbt.a:2lq
5n5u.a:7n8
5n5v.a is apo
1u7d.a is apo
1u7x.a is apo
4nd6.a is apo
5l7p.a:1pe
5l7p.b:buu
2pxh.a:bp5
5u36.b is apo
[1] 1j1u.a
0
1.8 1.4 0.9 4.5 1.6 2.4 2.2 1.7 0.6 - 1.4 - 2.6 - 1.3 3.0 4.0 3.9 4.9 1.9 - - - - 7.1 5.1 1.7 -
[1] 1zh0.a 0.1
0.1
0.3 0.2 1.9 1.3 0.4 0.5 0.8 0.3 - 0.6 - 2.5 - 0.4 2.7 2.2 2.2 2.9 0.8 - - - - 7.0 4.8 2.0 -
[1] 1zh6.a 0.1 0.1
0.1
0.2 1.5 1.6 0.5 0.5 0.6 0.1 - 1.4 - 2.8 - 0.8 2.9 1.8 1.7 2.8 0.9 - - - - 7.1 4.1 0.7 -
[1] 2ag6.a 0 0.1 0.2
0
2.2 1.3 0.3 0.4 1.1 0.3 - 1.3 - 2.8 - 0.7 2.8 2.2 2.2 3.2 0.7 - - - - 7.6 4.8 1.6 -
[1] 2hgz.a 0.1 0 0.2 0.1
0
1.9 0.2 0 0.7 0.1 - 1.4 - 2.5 - 0.7 2.9 0.5 0.4 1.8 0.4 - - - - 7.3 4.7 1.1 -
[1] 2zp1.a 0.1 1.8 1.6 0.8 5.0
0
2.6 2.8 2.3 1.2 - 0.3 - 0.3 - 0.3 0.3 4.5 4.7 5.8 2.2 - - - - 5.8 2.3 2.4 -
[1] 3d6u.a 0.2 0.3 0.2 0.1 1.4 2.6
0
0 0.5 0.1 - 1.9 - 2.9 - 1.5 2.8 1.5 1.5 2.5 0.5 - - - - 7.4 4.9 1.5 -
[1] 3d6v.a 0.1 0.2 0.1 0 0.9 2.6 0
0
0.7 0 - 1.7 - 2.7 - 1.4 2.8 1.0 1.1 2.1 0.4 - - - - 6.7 4.5 1.8 -
[1] 3n2y.a 0 0.3 0 0.2 1.8 1.8 0.6 0.4
0
0.1 - 1.1 - 2.6 - 0.7 2.8 1.5 1.7 2.2 0.1 - - - - 7.3 3.7 0.2 -
[1] 3qe4.b 0.1 0.2 0.2 0.1 2.2 1.6 0.6 0.9 0.2
0
- 1.3 - 2.8 - 0.5 2.8 2.0 2.2 2.7 0.1 - - - - 7.0 4.0 0.5 -
[1] 4hjr.a 0.9 1.8 1.6 1.5 4.0 1.1 3.7 3.5 2.5 1.0
-
1.2 - 0.1 - 1.5 1.1 4.0 3.9 4.8 2.5 - - - - 6.3 2.3 3.2 -
[1] 4hjx.a 0.2 0.5 0.7 0.5 2.1 0.2 1.8 1.9 1.8 1.0 -
0.1
- 0.2 - 0.5 0.2 3.7 3.9 4.3 1.7 - - - - 5.5 1.2 2.6 -
[1] 4hk4.a 0.6 1.0 1.5 1.1 3.5 1.4 1.8 1.6 1.5 0.7 - 1.1
-
0.7 - 1.1 0.9 2.6 2.6 3.9 0.9 - - - - 6.9 2.5 2.1 -
[1] 4hpw.a 0.1 0.6 0.8 0.3 3.1 0.8 1.4 1.2 0.8 0.1 - 0.3 -
0.2
- 0.6 0.5 2.3 2.0 3.6 0.1 - - - - 7.1 2.1 1.0 -
[1] 4nd7.a 0.2 0.3 0.3 0.2 3.3 0.6 1.0 1.3 0.8 0.2 - 0.5 - 0.8
-
0.3 1.0 3.5 3.5 3.6 0.6 - - - - 5.8 2.3 0.8 -
[1] 4nda.a 0 0.3 0.3 0.3 3.2 0.3 1.1 1.1 1.4 0.5 - 0.2 - 1.1 -
0
1.1 3.0 3.2 2.4 0.8 - - - - 6.5 2.0 1.1 -
[1] 4nx2.a 0.2 0.6 0.6 0.7 3.0 0.3 1.4 1.3 0.9 0.6 - 0.3 - 0.2 - 0.3
0
2.5 2.3 2.5 0.6 - - - - 4.2 0.8 1.4 -
[1] 4pbr.a 0.2 0.3 0.1 0.1 0.1 1.7 0.1 0 0.5 0 - 1.4 - 3.1 - 1.0 2.8
0
0 0.4 0.6 - - - - 5.9 4.1 1.6 -
[1] 4pbs.a 0.3 0.4 0.2 0.2 0 1.8 0.2 0 0.5 0 - 1.3 - 2.6 - 1.0 2.6 0.2
0
1.2 0.6 - - - - 5.8 4.7 1.1 -
[1] 4pbt.a 0.2 0.3 0.1 0.2 0 1.7 0 0 0.4 0.2 - 1.4 - 2.9 - 1.0 2.9 0 0
0
0.6 - - - - 5.2 4.2 1.2 -
[1] 5n5u.a 0.4 0.7 0.5 0.5 1.8 1.1 0.9 0.5 1.0 0.3 - 1.1 - 1.9 - 0.7 1.8 2.2 1.9 3.2
0
- - - - 6.0 3.3 2.0 -
[1] 5n5v.a 0.2 0.5 0.5 0.3 1.5 1.0 0.7 0.7 0.9 0.2 - 0.8 - 1.9 - 0.8 1.9 2.2 1.9 3.3 0
-
- - - 5.7 3.0 1.3 -
[2] 1u7d.a 0.1 1.8 1.4 0.8 4.4 0.4 2.6 2.5 1.9 0.6 - 0.6 - 0.5 - 1.2 1.3 4.3 3.8 4.9 1.9 -
-
- - 4.0 4.1 1.6 -
[2] 1u7x.a 0.6 0.9 0.9 0.9 2.4 0.6 1.1 1.4 1.5 0.7 - 0.7 - 0.2 - 0.6 0.4 2.6 2.6 4.2 1.1 - -
-
- 1.8 2.7 1.6 -
[2] 4nd6.a 0.5 0.9 0.5 0.7 3.3 0.6 1.3 1.6 0.7 0.5 - 0.8 - 0.6 - 0.3 0.6 3.5 3.2 3.0 0.4 - - -
-
0.9 2.1 0.6 -
[3] 5l7p.a 0.3 0.6 0.4 0.3 0.9 0.6 0.6 0.6 0.5 0.2 - 0.8 - 0.4 - 0.2 0.5 1.1 1.1 2.6 0.4 - - - -
0
0.6 0.5 -
[3] 5l7p.b 0 0.1 0.2 0.1 1.0 0 0.2 0.3 0.4 0.1 - 0.1 - 0.2 - 0 0.1 0.9 1.0 2.4 0.3 - - - - 4.3
0
0.6 -
[4] 2pxh.a 0.1 2.1 0.4 0.2 2.9 0.4 1.4 1.4 0.4 0.1 - 0.1 - 0.2 - 0 0.1 3.4 2.7 3.8 0.1 - - - - 5.8 1.6
0
-
[5] 5u36.b 0.7 0.9 1.5 0.7 1.8 0.6 1.5 0.9 1.6 1.0 - 0.6 - 0.8 - 0.6 0.3 1.7 2.2 4.6 0.8 - - - - 2.6 1.5 1.2
-
[Pocket-ligand steric clashes matrix]

Pocket clash dissimilarity (5 clusters)

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
1j1u.a
1zh0.a
1zh6.a
2ag6.a
2hgz.a
2zp1.a
3d6u.a
3d6v.a
3n2y.a
3qe4.b
4hjr.a
4hjx.a
4hk4.a
4hpw.a
4nd7.a
4nda.a
4nx2.a
4pbr.a
4pbs.a
4pbt.a
5n5u.a
5n5v.a
1u7d.a
1u7x.a
4nd6.a
5l7p.a
5l7p.b
2pxh.a
5u36.b
[1] 1j1u.a
0
.20 .17 .22 .16 .11 .23 .24 .15 .14 .21 .19 .25 .25 .17 .16 .22 .21 .19 .22 .20 .22 .19 .29 .32 .40 .27 .38 .59
[1] 1zh0.a .20
0
.11 .05 .18 .29 .08 .08 .12 .14 .29 .25 .33 .32 .17 .18 .26 .15 .15 .15 .23 .24 .36 .29 .32 .40 .29 .33 .47
[1] 1zh6.a .17 .11
0
.10 .14 .25 .08 .12 .09 .11 .26 .21 .29 .29 .16 .15 .22 .11 .13 .11 .18 .19 .34 .27 .30 .36 .24 .28 .49
[1] 2ag6.a .22 .05 .10
0
.20 .31 .06 .09 .15 .15 .31 .27 .34 .34 .18 .19 .28 .18 .18 .18 .25 .26 .38 .32 .35 .43 .31 .35 .49
[1] 2hgz.a .16 .18 .14 .20
0
.23 .17 .19 .11 .13 .30 .27 .28 .25 .22 .22 .25 .08 .07 .11 .11 .13 .31 .33 .36 .31 .16 .27 .52
[1] 2zp1.a .11 .29 .25 .31 .23
0
.32 .33 .23 .23 .15 .15 .20 .17 .17 .14 .19 .28 .27 .31 .22 .25 .23 .27 .30 .37 .23 .35 .55
[1] 3d6u.a .23 .08 .08 .06 .17 .32
0
.05 .13 .15 .32 .28 .34 .34 .21 .21 .27 .15 .17 .15 .22 .24 .40 .34 .35 .40 .28 .33 .48
[1] 3d6v.a .24 .08 .12 .09 .19 .33 .05
0
.14 .14 .31 .29 .34 .35 .21 .21 .26 .16 .19 .15 .24 .24 .42 .35 .35 .38 .27 .34 .45
[1] 3n2y.a .15 .12 .09 .15 .11 .23 .13 .14
0
.08 .24 .20 .24 .24 .17 .17 .19 .10 .09 .11 .15 .17 .31 .29 .31 .30 .18 .28 .50
[1] 3qe4.b .14 .14 .11 .15 .13 .23 .15 .14 .08
0
.23 .22 .24 .24 .16 .17 .17 .12 .13 .14 .17 .18 .32 .29 .29 .33 .21 .30 .51
[1] 4hjr.a .21 .29 .26 .31 .30 .15 .32 .31 .24 .23
0
.08 .13 .14 .16 .14 .10 .27 .29 .31 .28 .30 .31 .23 .25 .31 .22 .33 .48
[1] 4hjx.a .19 .25 .21 .27 .27 .15 .28 .29 .20 .22 .08
0
.16 .16 .13 .11 .11 .23 .27 .25 .26 .29 .29 .22 .24 .29 .18 .31 .43
[1] 4hk4.a .25 .33 .29 .34 .28 .20 .34 .34 .24 .24 .13 .16
0
.07 .21 .19 .12 .31 .31 .35 .24 .27 .35 .30 .29 .29 .19 .35 .46
[1] 4hpw.a .25 .32 .29 .34 .25 .17 .34 .35 .24 .24 .14 .16 .07
0
.21 .20 .12 .30 .29 .34 .22 .26 .34 .29 .29 .28 .17 .34 .48
[1] 4nd7.a .17 .17 .16 .18 .22 .17 .21 .21 .17 .16 .16 .13 .21 .21
0
.06 .15 .19 .19 .19 .21 .21 .29 .16 .18 .32 .20 .25 .47
[1] 4nda.a .16 .18 .15 .19 .22 .14 .21 .21 .17 .17 .14 .11 .19 .20 .06
0
.14 .19 .22 .20 .21 .23 .27 .19 .23 .35 .22 .29 .46
[1] 4nx2.a .22 .26 .22 .28 .25 .19 .27 .26 .19 .17 .10 .11 .12 .12 .15 .14
0
.24 .26 .25 .23 .25 .32 .22 .23 .24 .15 .27 .39
[1] 4pbr.a .21 .15 .11 .18 .08 .28 .15 .16 .10 .12 .27 .23 .31 .30 .19 .19 .24
0
.06 .05 .17 .19 .36 .31 .32 .30 .19 .22 .50
[1] 4pbs.a .19 .15 .13 .18 .07 .27 .17 .19 .09 .13 .29 .27 .31 .29 .19 .22 .26 .06
0
.08 .14 .16 .34 .30 .31 .27 .18 .22 .54
[1] 4pbt.a .22 .15 .11 .18 .11 .31 .15 .15 .11 .14 .31 .25 .35 .34 .19 .20 .25 .05 .08
0
.20 .21 .38 .32 .30 .28 .20 .23 .48
[1] 5n5u.a .20 .23 .18 .25 .11 .22 .22 .24 .15 .17 .28 .26 .24 .22 .21 .21 .23 .17 .14 .20
0
.04 .31 .30 .34 .31 .18 .28 .48
[1] 5n5v.a .22 .24 .19 .26 .13 .25 .24 .24 .17 .18 .30 .29 .27 .26 .21 .23 .25 .19 .16 .21 .04
0
.32 .31 .34 .31 .19 .30 .50
[2] 1u7d.a .19 .36 .34 .38 .31 .23 .40 .42 .31 .32 .31 .29 .35 .34 .29 .27 .32 .36 .34 .38 .31 .32
0
.19 .22 .29 .38 .49 .48
[2] 1u7x.a .29 .29 .27 .32 .33 .27 .34 .35 .29 .29 .23 .22 .30 .29 .16 .19 .22 .31 .30 .32 .30 .31 .19
0
.08 .21 .33 .36 .38
[2] 4nd6.a .32 .32 .30 .35 .36 .30 .35 .35 .31 .29 .25 .24 .29 .29 .18 .23 .23 .32 .31 .30 .34 .34 .22 .08
0
.16 .31 .32 .37
[3] 5l7p.a .40 .40 .36 .43 .31 .37 .40 .38 .30 .33 .31 .29 .29 .28 .32 .35 .24 .30 .27 .28 .31 .31 .29 .21 .16
0
.16 .32 .31
[3] 5l7p.b .27 .29 .24 .31 .16 .23 .28 .27 .18 .21 .22 .18 .19 .17 .20 .22 .15 .19 .18 .20 .18 .19 .38 .33 .31 .16
0
.24 .41
[4] 2pxh.a .38 .33 .28 .35 .27 .35 .33 .34 .28 .30 .33 .31 .35 .34 .25 .29 .27 .22 .22 .23 .28 .30 .49 .36 .32 .32 .24
0
.52
[5] 5u36.b .59 .47 .49 .49 .52 .55 .48 .45 .50 .51 .48 .43 .46 .48 .47 .46 .39 .50 .54 .48 .48 .50 .48 .38 .37 .31 .41 .52
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 1.8 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
1j1u.a
1zh0.a
1zh6.a
2ag6.a
2hgz.a
2zp1.a
3d6u.a
3d6v.a
3n2y.a
3qe4.b
4hjr.a
4hjx.a
4hk4.a
4hpw.a
4nd7.a
4nda.a
4nx2.a
4pbr.a
4pbs.a
4pbt.a
5n5u.a
5n5v.a
1u7d.a
1u7x.a
4nd6.a
5l7p.a
5l7p.b
2pxh.a
5u36.b
[1] 1j1u.a
0
1.6 1.1 1.6 0.4 0.3 1.6 1.7 0.3 0.4 0.9 0.9 0.7 0.7 0.4 0.3 0.6 0.3 0.3 0.4 0.5 0.5 1.7 1.9 2.1 1.8 0.4 0.5 3.5
[1] 1zh0.a 1.6
0
1.6 0.3 1.6 1.6 0.3 0.4 1.6 1.7 1.8 1.8 1.6 1.7 1.7 1.7 1.7 1.6 1.6 1.7 1.6 1.6 2.3 2.5 2.6 2.4 1.7 1.6 3.5
[1] 1zh6.a 1.1 1.6
0
1.6 1.1 1.0 1.6 1.6 1.1 1.1 1.3 1.5 1.1 1.2 1.2 1.1 1.1 1.1 1.1 1.3 1.1 1.1 2.0 2.2 2.4 2.1 1.1 1.2 3.5
[1] 2ag6.a 1.6 0.3 1.6
0
1.6 1.6 0.2 0.3 1.6 1.6 1.8 1.8 1.7 1.7 1.6 1.6 1.7 1.6 1.6 1.7 1.6 1.6 2.3 2.5 2.6 2.4 1.6 1.6 3.6
[1] 2hgz.a 0.4 1.6 1.1 1.6
0
0.4 1.6 1.7 0.3 0.6 0.9 1.0 0.5 0.5 0.5 0.5 0.7 0.4 0.3 0.6 0.4 0.4 1.7 1.9 2.1 1.8 0.6 0.3 3.5
[1] 2zp1.a 0.3 1.6 1.0 1.6 0.4
0
1.6 1.7 0.4 0.4 1.0 1.0 0.7 0.8 0.4 0.3 0.7 0.4 0.3 0.5 0.6 0.5 1.7 1.9 2.1 1.9 0.3 0.6 3.5
[1] 3d6u.a 1.6 0.3 1.6 0.2 1.6 1.6
0
0.3 1.6 1.7 1.8 1.8 1.7 1.7 1.6 1.6 1.7 1.6 1.6 1.7 1.6 1.7 2.3 2.5 2.6 2.4 1.6 1.6 3.6
[1] 3d6v.a 1.7 0.4 1.6 0.3 1.7 1.7 0.3
0
1.7 1.7 1.8 1.9 1.8 1.8 1.7 1.7 1.8 1.7 1.7 1.8 1.7 1.7 2.3 2.5 2.6 2.4 1.7 1.7 3.6
[1] 3n2y.a 0.3 1.6 1.1 1.6 0.3 0.4 1.6 1.7
0
0.5 0.9 0.9 0.6 0.6 0.5 0.4 0.6 0.3 0.3 0.5 0.4 0.5 1.7 1.9 2.1 1.8 0.5 0.4 3.5
[1] 3qe4.b 0.4 1.7 1.1 1.6 0.6 0.4 1.7 1.7 0.5
0
0.9 1.0 0.7 0.7 0.5 0.5 0.6 0.5 0.4 0.6 0.6 0.6 1.7 1.9 2.1 1.8 0.4 0.7 3.6
[1] 4hjr.a 0.9 1.8 1.3 1.8 0.9 1.0 1.8 1.8 0.9 0.9
0
0.8 0.8 0.8 1.0 1.0 0.8 0.9 0.9 1.0 0.8 0.9 2.0 2.1 2.3 2.0 1.1 0.9 3.5
[1] 4hjx.a 0.9 1.8 1.5 1.8 1.0 1.0 1.8 1.9 0.9 1.0 0.8
0
1.1 1.1 1.0 1.0 1.0 0.9 1.0 1.0 1.0 1.1 2.0 2.2 2.3 2.1 1.1 1.0 3.5
[1] 4hk4.a 0.7 1.6 1.1 1.7 0.5 0.7 1.7 1.8 0.6 0.7 0.8 1.1
0
0.2 0.8 0.8 0.8 0.7 0.6 0.9 0.4 0.6 1.9 2.0 2.2 1.9 0.9 0.5 3.5
[1] 4hpw.a 0.7 1.7 1.2 1.7 0.5 0.8 1.7 1.8 0.6 0.7 0.8 1.1 0.2
0
0.8 0.8 0.8 0.7 0.6 0.9 0.4 0.6 1.8 2.0 2.2 1.9 0.9 0.4 3.5
[1] 4nd7.a 0.4 1.7 1.2 1.6 0.5 0.4 1.6 1.7 0.5 0.5 1.0 1.0 0.8 0.8
0
0.4 0.7 0.3 0.4 0.3 0.6 0.5 1.7 1.9 2.1 1.8 0.4 0.6 3.6
[1] 4nda.a 0.3 1.7 1.1 1.6 0.5 0.3 1.6 1.7 0.4 0.5 1.0 1.0 0.8 0.8 0.4
0
0.7 0.4 0.4 0.5 0.7 0.6 1.8 2.0 2.1 1.9 0.4 0.6 3.5
[1] 4nx2.a 0.6 1.7 1.1 1.7 0.7 0.7 1.7 1.8 0.6 0.6 0.8 1.0 0.8 0.8 0.7 0.7
0
0.6 0.6 0.7 0.7 0.7 1.8 2.0 2.2 1.9 0.7 0.7 3.5
[1] 4pbr.a 0.3 1.6 1.1 1.6 0.4 0.4 1.6 1.7 0.3 0.5 0.9 0.9 0.7 0.7 0.3 0.4 0.6
0
0.2 0.3 0.5 0.5 1.7 1.9 2.1 1.8 0.4 0.4 3.6
[1] 4pbs.a 0.3 1.6 1.1 1.6 0.3 0.3 1.6 1.7 0.3 0.4 0.9 1.0 0.6 0.6 0.4 0.4 0.6 0.2
0
0.4 0.4 0.4 1.7 1.9 2.1 1.8 0.4 0.4 3.5
[1] 4pbt.a 0.4 1.7 1.3 1.7 0.6 0.5 1.7 1.8 0.5 0.6 1.0 1.0 0.9 0.9 0.3 0.5 0.7 0.3 0.4
0
0.7 0.6 1.7 1.9 2.0 1.8 0.5 0.6 3.6
[1] 5n5u.a 0.5 1.6 1.1 1.6 0.4 0.6 1.6 1.7 0.4 0.6 0.8 1.0 0.4 0.4 0.6 0.7 0.7 0.5 0.4 0.7
0
0.4 1.7 1.9 2.1 1.8 0.7 0.4 3.5
[1] 5n5v.a 0.5 1.6 1.1 1.6 0.4 0.5 1.7 1.7 0.5 0.6 0.9 1.1 0.6 0.6 0.5 0.6 0.7 0.5 0.4 0.6 0.4
0
1.6 1.9 2.1 1.7 0.7 0.5 3.4
[2] 1u7d.a 1.7 2.3 2.0 2.3 1.7 1.7 2.3 2.3 1.7 1.7 2.0 2.0 1.9 1.8 1.7 1.8 1.8 1.7 1.7 1.7 1.7 1.6
0
0.8 0.8 0.8 1.7 1.8 2.9
[2] 1u7x.a 1.9 2.5 2.2 2.5 1.9 1.9 2.5 2.5 1.9 1.9 2.1 2.2 2.0 2.0 1.9 2.0 2.0 1.9 1.9 1.9 1.9 1.9 0.8
0
0.8 1.1 1.9 2.0 3.2
[2] 4nd6.a 2.1 2.6 2.4 2.6 2.1 2.1 2.6 2.6 2.1 2.1 2.3 2.3 2.2 2.2 2.1 2.1 2.2 2.1 2.1 2.0 2.1 2.1 0.8 0.8
0
1.1 2.1 2.2 3.5
[3] 5l7p.a 1.8 2.4 2.1 2.4 1.8 1.9 2.4 2.4 1.8 1.8 2.0 2.1 1.9 1.9 1.8 1.9 1.9 1.8 1.8 1.8 1.8 1.7 0.8 1.1 1.1
0
1.8 1.9 3.2
[3] 5l7p.b 0.4 1.7 1.1 1.6 0.6 0.3 1.6 1.7 0.5 0.4 1.1 1.1 0.9 0.9 0.4 0.4 0.7 0.4 0.4 0.5 0.7 0.7 1.7 1.9 2.1 1.8
0
0.7 3.6
[4] 2pxh.a 0.5 1.6 1.2 1.6 0.3 0.6 1.6 1.7 0.4 0.7 0.9 1.0 0.5 0.4 0.6 0.6 0.7 0.4 0.4 0.6 0.4 0.5 1.8 2.0 2.2 1.9 0.7
0
3.5
[5] 5u36.b 3.5 3.5 3.5 3.6 3.5 3.5 3.6 3.6 3.5 3.6 3.5 3.5 3.5 3.5 3.6 3.5 3.5 3.6 3.5 3.6 3.5 3.4 2.9 3.2 3.5 3.2 3.6 3.5
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 1.1 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
1j1u.a
1zh0.a
1zh6.a
2ag6.a
2hgz.a
2zp1.a
3d6u.a
3d6v.a
3n2y.a
3qe4.b
4hjr.a
4hjx.a
4hk4.a
4hpw.a
4nd7.a
4nda.a
4nx2.a
4pbr.a
4pbs.a
4pbt.a
5n5u.a
5n5v.a
1u7d.a
1u7x.a
4nd6.a
5l7p.a
5l7p.b
2pxh.a
5u36.b
[1] 1j1u.a
0
2.6 1.5 2.7 0.7 0.5 2.8 2.8 0.6 0.8 0.9 1.2 1.0 1.0 1.0 1.0 0.9 1.0 0.9 0.9 1.0 1.1 1.9 2.4 2.3 2.1 0.9 0.9 4.5
[1] 1zh0.a 2.6
0
2.4 0.5 2.2 2.6 0.6 0.7 2.6 2.7 2.8 2.8 2.7 2.6 2.8 2.8 2.8 2.7 2.7 2.8 2.8 2.8 3.3 3.4 3.5 3.3 2.8 2.6 4.3
[1] 1zh6.a 1.5 2.4
0
2.4 1.3 1.3 2.4 2.4 1.4 1.5 1.6 2.1 1.7 1.7 1.9 1.8 1.6 2.0 1.6 1.9 1.9 2.0 2.3 2.7 2.8 2.5 1.7 1.8 4.6
[1] 2ag6.a 2.7 0.5 2.4
0
2.2 2.6 0.7 0.7 2.7 2.7 2.9 2.9 2.8 2.8 2.8 2.8 2.9 2.9 2.7 3.0 3.0 3.0 3.4 3.5 3.5 3.4 2.8 2.8 4.4
[1] 2hgz.a 0.7 2.2 1.3 2.2
0
0.8 2.2 2.3 0.6 0.9 1.0 1.1 0.7 0.6 1.0 0.9 1.0 0.8 0.9 0.9 0.8 0.9 2.0 2.4 2.3 2.2 1.0 0.5 4.5
[1] 2zp1.a 0.5 2.6 1.3 2.6 0.8
0
2.6 2.6 0.6 0.8 1.0 1.4 1.1 1.1 1.1 1.0 1.0 1.2 0.9 1.0 1.2 1.2 2.0 2.2 2.3 2.2 0.9 1.0 4.5
[1] 3d6u.a 2.8 0.6 2.4 0.7 2.2 2.6
0
0.4 2.7 2.7 2.9 2.9 2.8 2.8 2.9 2.8 2.9 2.9 2.7 3.0 3.0 3.0 3.4 3.5 3.5 3.3 2.8 2.8 4.4
[1] 3d6v.a 2.8 0.7 2.4 0.7 2.3 2.6 0.4
0
2.7 2.7 2.9 2.9 2.8 2.8 2.8 2.8 2.9 2.8 2.7 2.9 3.0 3.0 3.4 3.5 3.5 3.3 2.8 2.8 4.4
[1] 3n2y.a 0.6 2.6 1.4 2.7 0.6 0.6 2.7 2.7
0
0.8 0.9 1.3 1.0 1.0 1.0 1.0 0.9 1.1 0.9 1.0 1.1 1.1 2.0 2.4 2.3 2.1 0.9 0.9 4.6
[1] 3qe4.b 0.8 2.7 1.5 2.7 0.9 0.8 2.7 2.7 0.8
0
1.0 1.4 1.0 1.0 0.9 0.9 0.9 1.2 0.9 1.1 1.0 1.1 2.0 2.4 2.3 2.2 0.8 1.0 4.6
[1] 4hjr.a 0.9 2.8 1.6 2.9 1.0 1.0 2.9 2.9 0.9 1.0
0
1.4 1.0 1.0 1.2 1.2 0.9 1.3 1.1 1.2 1.1 1.2 2.1 2.3 2.4 2.3 1.2 1.3 4.4
[1] 4hjx.a 1.2 2.8 2.1 2.9 1.1 1.4 2.9 2.9 1.3 1.4 1.4
0
1.1 1.1 1.4 1.4 1.5 1.1 1.5 1.3 1.2 1.2 2.3 2.5 2.5 2.5 1.4 1.3 4.3
[1] 4hk4.a 1.0 2.7 1.7 2.8 0.7 1.1 2.8 2.8 1.0 1.0 1.0 1.1
0
0.4 1.2 1.1 1.1 1.1 1.1 1.2 0.9 1.0 2.2 2.4 2.4 2.3 1.2 0.7 4.3
[1] 4hpw.a 1.0 2.6 1.7 2.8 0.6 1.1 2.8 2.8 1.0 1.0 1.0 1.1 0.4
0
1.1 1.1 1.1 1.0 1.1 1.1 0.8 0.9 2.2 2.4 2.4 2.3 1.2 0.7 4.3
[1] 4nd7.a 1.0 2.8 1.9 2.8 1.0 1.1 2.9 2.8 1.0 0.9 1.2 1.4 1.2 1.1
0
0.7 0.9 0.8 0.7 0.6 0.8 0.8 2.0 2.2 2.1 2.1 0.7 1.1 4.5
[1] 4nda.a 1.0 2.8 1.8 2.8 0.9 1.0 2.8 2.8 1.0 0.9 1.2 1.4 1.1 1.1 0.7
0
0.9 0.8 0.7 0.7 0.8 0.8 2.1 2.2 2.2 2.2 0.7 1.1 4.5
[1] 4nx2.a 0.9 2.8 1.6 2.9 1.0 1.0 2.9 2.9 0.9 0.9 0.9 1.5 1.1 1.1 0.9 0.9
0
1.1 0.8 0.9 1.0 1.1 2.0 2.2 2.3 2.1 0.9 1.2 4.4
[1] 4pbr.a 1.0 2.7 2.0 2.9 0.8 1.2 2.9 2.8 1.1 1.2 1.3 1.1 1.1 1.0 0.8 0.8 1.1
0
0.9 0.6 0.7 0.7 2.1 2.4 2.3 2.2 0.8 0.9 4.5
[1] 4pbs.a 0.9 2.7 1.6 2.7 0.9 0.9 2.7 2.7 0.9 0.9 1.1 1.5 1.1 1.1 0.7 0.7 0.8 0.9
0
0.8 0.8 0.9 1.9 2.3 2.2 2.0 0.7 1.1 4.6
[1] 4pbt.a 0.9 2.8 1.9 3.0 0.9 1.0 3.0 2.9 1.0 1.1 1.2 1.3 1.2 1.1 0.6 0.7 0.9 0.6 0.8
0
0.9 0.9 2.0 2.4 2.2 2.1 0.7 1.0 4.6
[1] 5n5u.a 1.0 2.8 1.9 3.0 0.8 1.2 3.0 3.0 1.1 1.0 1.1 1.2 0.9 0.8 0.8 0.8 1.0 0.7 0.8 0.9
0
0.5 2.0 2.3 2.2 2.2 0.9 0.9 4.3
[1] 5n5v.a 1.1 2.8 2.0 3.0 0.9 1.2 3.0 3.0 1.1 1.1 1.2 1.2 1.0 0.9 0.8 0.8 1.1 0.7 0.9 0.9 0.5
0
2.0 2.2 2.2 2.2 0.9 1.0 4.3
[2] 1u7d.a 1.9 3.3 2.3 3.4 2.0 2.0 3.4 3.4 2.0 2.0 2.1 2.3 2.2 2.2 2.0 2.1 2.0 2.1 1.9 2.0 2.0 2.0
0
1.3 1.4 1.3 2.0 2.1 4.2
[2] 1u7x.a 2.4 3.4 2.7 3.5 2.4 2.2 3.5 3.5 2.4 2.4 2.3 2.5 2.4 2.4 2.2 2.2 2.2 2.4 2.3 2.4 2.3 2.2 1.3
0
1.3 1.6 2.2 2.4 4.5
[2] 4nd6.a 2.3 3.5 2.8 3.5 2.3 2.3 3.5 3.5 2.3 2.3 2.4 2.5 2.4 2.4 2.1 2.2 2.3 2.3 2.2 2.2 2.2 2.2 1.4 1.3
0
1.5 2.2 2.4 4.8
[3] 5l7p.a 2.1 3.3 2.5 3.4 2.2 2.2 3.3 3.3 2.1 2.2 2.3 2.5 2.3 2.3 2.1 2.2 2.1 2.2 2.0 2.1 2.2 2.2 1.3 1.6 1.5
0
2.1 2.3 4.4
[3] 5l7p.b 0.9 2.8 1.7 2.8 1.0 0.9 2.8 2.8 0.9 0.8 1.2 1.4 1.2 1.2 0.7 0.7 0.9 0.8 0.7 0.7 0.9 0.9 2.0 2.2 2.2 2.1
0
1.1 4.5
[4] 2pxh.a 0.9 2.6 1.8 2.8 0.5 1.0 2.8 2.8 0.9 1.0 1.3 1.3 0.7 0.7 1.1 1.1 1.2 0.9 1.1 1.0 0.9 1.0 2.1 2.4 2.4 2.3 1.1
0
4.4
[5] 5u36.b 4.5 4.3 4.6 4.4 4.5 4.5 4.4 4.4 4.6 4.6 4.4 4.3 4.3 4.3 4.5 4.5 4.4 4.5 4.6 4.6 4.3 4.3 4.2 4.5 4.8 4.4 4.5 4.4
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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