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SYW_GEOSE_1_327

Tryptophan--tRNA ligase [Class-I aminoacyl-tRNA synthetase family]

Composition of the binding site

Protein chains monomer
A1 (SYW_GEOSE):5:9, 11, 15:25, 40, 43, 107, 111, 125, 129, 132, 133, 141, 143:147, 150, 176, 177, 179:183, 192:197, 244, 2475:9, 11, 15:25, 40, 43, 107, 111, 125, 129, 132, 133, 141, 143:147, 150, 176, 177, 179:183, 192:197, 244, 247

Full PDB list

1d2r, 1i6k, 1i6l, 1i6m, 1m83, 1mau, 1maw, 1mb2, 2ov4, 3fhj, 3u1v, 5dk4 (redundant Pocketome entry)

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1
F
5
S
6
G
7
I
8
Q
9
S
1
1
G
1
7
N
1
8
G
2
1
A
2
2
V
4
0
H
4
3
K
1
1
1
Y
1
2
5
M
1
2
9
D
1
3
2
I
1
3
3
V
1
4
1
V
1
4
3
G
1
4
4
D
1
4
6
Q
1
4
7
I
1
7
6
G
1
8
0
A
1
8
1
R
1
8
2
I
1
8
3
K
1
9
2
M
1
9
3
S
1
9
4
K
1
9
5
S
1
9
6
[1]1i6k.a tym37 . . . . . . . . . . . . . . * . . . . . . . . . . . . . * . . .
[1]1i6m.a tym37 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]1m83.a atp31 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]1mau.a atp,ltn46 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]2ov4.a anl,aqp42 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]5dk4.a 5bx,atp50 . . . . . . . . . . . . . . * . . . . . . . . . . . . . * . . .
[2]1d2r.b none . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[2]1mb2.a W15 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[2]3fhj.a amp,W38 . . . . . - . . . . . . - . . . . . . . . . . . . . . . . . . .
[2]3u1v.a none . . A . C T . R . . A S L H Y * . . . . Y G . . . . . S * Y Q .
[2]3u1v.d none . . A . C T . R . . A S L H Y * . . . . Y G . . . . . - - - - -

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

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PDB.ch
A1
F
5
S
6
G
7
I
8
Q
9
S
1
1
T
1
5
I
1
6
G
1
7
N
1
8
Y
1
9
I
2
0
G
2
1
A
2
2
L
2
3
R
2
4
Q
2
5
V
4
0
H
4
3
Q
1
0
7
K
1
1
1
Y
1
2
5
M
1
2
9
D
1
3
2
I
1
3
3
V
1
4
1
V
1
4
3
G
1
4
4
E
1
4
5
D
1
4
6
Q
1
4
7
H
1
5
0
I
1
7
6
P
1
7
7
V
1
7
9
G
1
8
0
A
1
8
1
R
1
8
2
I
1
8
3
K
1
9
2
M
1
9
3
S
1
9
4
K
1
9
5
S
1
9
6
D
1
9
7
I
2
4
4
T
2
4
7
[1]1i6k.a . . . . . . . . * . . * * * . . . . . . . * * . . . . . . . . . . . . . . . . . * . . . . . .
[1]1i6m.a . . . . . . . . * . . * * . . . . . . . . * . . . . . . . . . . . . . . . . . . . . * . . . .
[1]1m83.a . . . . . . . . * . . * * * . . . . . . . * . . . . . . . . . . . . . . . . * . . . . . . . .
[1]1mau.a . . . . . . . . * . . * * * . . . . . . . * . . . . . . . . . . . . . . . . * . . . . . . . .
[1]2ov4.a . . . . . . . . * . . * * * . . . . . . . * . . . . . . . . * . . . . . . . * . . . . . . . .
[1]5dk4.a . . . . . . . . * . . * * * . . . . . . . . * . . . . . . . . . . . . . . . * . * . . . . . .
[2]1d2r.b . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . * . . . . . . .
[2]1mb2.a . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . * . . . . . . .
[2]3fhj.a . . . . . - . . . . . . . . . . . . . . - . . . . . . . . . . . . . . . . . . * . . . . . . .
[2]3u1v.a . . A . C T . . . R . . . . . . . A S L L H Y mse . . . . . Y G L . . . . . * . S * Y Q . . . .
[2]3u1v.d . . A . C T . . . R . . . . . . . A S L L H Y mse . . . . . Y G L . . . . . * . - - - - - . . .

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
1i6k.a:tym
1i6m.a:tym
1m83.a:atp
1mau.a:atp,ltn
2ov4.a:anl,aqp
5dk4.a:5bx,atp
1d2r.b is apo
1mb2.a:W
3fhj.a:W,amp
3u1v.a is apo
3u1v.d is apo
[1] 1i6k.a
0.1
0.1 0.5 1.3 1.2 3.7 - 0.4 7.2 - -
[1] 1i6m.a 0.1
0
1.5 1.9 1.5 4.2 - 0.5 6.8 - -
[1] 1m83.a 0.5 0.4
0.2
0.7 0.7 3.1 - 0.6 7.0 - -
[1] 1mau.a 0.4 0.4 0.2
0.2
0.6 2.6 - 0.4 6.5 - -
[1] 2ov4.a 0.5 0.5 0.4 1.1
0.7
3.7 - 0.7 6.8 - -
[1] 5dk4.a 0.4 0.3 0.1 0 0.5
0.1
- 0 6.4 - -
[2] 1d2r.b 1.1 1.1 1.1 1.3 1.0 1.4
-
0.1 0.1 - -
[2] 1mb2.a 0.8 0.7 0.7 0.7 0.8 0.8 -
0
0 - -
[2] 3fhj.a 1.7 1.7 1.3 1.3 1.3 1.3 - 0
0.1
- -
[2] 3u1v.a 2.4 2.8 1.5 2.2 2.4 2.4 - 0.8 3.3
-
-
[2] 3u1v.d 2.7 2.7 1.5 2.6 3.6 2.9 - 1.6 6.1 -
-
[Pocket-ligand steric clashes matrix]

Pocket clash dissimilarity (2 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
1i6k.a
1i6m.a
1m83.a
1mau.a
2ov4.a
5dk4.a
1d2r.b
1mb2.a
3fhj.a
3u1v.a
3u1v.d
[1] 1i6k.a
0
.03 .05 .06 .08 .12 .25 .25 .27 .29 .36
[1] 1i6m.a .03
0
.07 .08 .10 .14 .26 .26 .27 .29 .36
[1] 1m83.a .05 .07
0
.03 .05 .09 .23 .23 .25 .28 .35
[1] 1mau.a .06 .08 .03
0
.05 .08 .23 .22 .23 .26 .33
[1] 2ov4.a .08 .10 .05 .05
0
.10 .25 .24 .26 .29 .36
[1] 5dk4.a .12 .14 .09 .08 .10
0
.18 .17 .18 .22 .29
[2] 1d2r.b .25 .26 .23 .23 .25 .18
0
.02 .03 .12 .18
[2] 1mb2.a .25 .26 .23 .22 .24 .17 .02
0
.03 .11 .17
[2] 3fhj.a .27 .27 .25 .23 .26 .18 .03 .03
0
.13 .19
[2] 3u1v.a .29 .29 .28 .26 .29 .22 .12 .11 .13
0
.10
[2] 3u1v.d .36 .36 .35 .33 .36 .29 .18 .17 .19 .10
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 2.9 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
1i6k.a
1i6m.a
1m83.a
1mau.a
2ov4.a
5dk4.a
1d2r.b
1mb2.a
3fhj.a
3u1v.a
3u1v.d
[1] 1i6k.a
0
0.1 1.1 1.0 1.1 1.1 4.0 3.9 4.0 3.6 3.3
[1] 1i6m.a 0.1
0
1.1 1.0 1.1 1.1 4.0 3.9 4.0 3.6 3.3
[1] 1m83.a 1.1 1.1
0
0.2 0.3 0.3 4.3 4.2 4.2 4.0 3.5
[1] 1mau.a 1.0 1.0 0.2
0
0.3 0.3 4.3 4.2 4.2 4.0 3.5
[1] 2ov4.a 1.1 1.1 0.3 0.3
0
0.3 4.2 4.2 4.2 4.0 3.5
[1] 5dk4.a 1.1 1.1 0.3 0.3 0.3
0
4.3 4.2 4.2 4.1 3.5
[2] 1d2r.b 4.0 4.0 4.3 4.3 4.2 4.3
0
1.1 1.7 1.6 1.9
[2] 1mb2.a 3.9 3.9 4.2 4.2 4.2 4.2 1.1
0
1.7 1.6 2.0
[2] 3fhj.a 4.0 4.0 4.2 4.2 4.2 4.2 1.7 1.7
0
1.8 2.4
[2] 3u1v.a 3.6 3.6 4.0 4.0 4.0 4.1 1.6 1.6 1.8
0
1.2
[2] 3u1v.d 3.3 3.3 3.5 3.5 3.5 3.5 1.9 2.0 2.4 1.2
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 2.4 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
1i6k.a
1i6m.a
1m83.a
1mau.a
2ov4.a
5dk4.a
1d2r.b
1mb2.a
3fhj.a
3u1v.a
3u1v.d
[1] 1i6k.a
0
0.4 1.4 1.3 1.3 1.5 4.3 4.1 4.1 4.2 3.8
[1] 1i6m.a 0.4
0
1.4 1.3 1.4 1.5 4.3 4.2 4.1 4.1 3.8
[1] 1m83.a 1.4 1.4
0
0.4 0.4 0.9 4.5 4.3 4.3 4.4 3.9
[1] 1mau.a 1.3 1.3 0.4
0
0.5 0.9 4.5 4.3 4.3 4.4 3.9
[1] 2ov4.a 1.3 1.4 0.4 0.5
0
0.9 4.4 4.2 4.2 4.3 3.9
[1] 5dk4.a 1.5 1.5 0.9 0.9 0.9
0
4.4 4.2 4.2 4.4 3.9
[2] 1d2r.b 4.3 4.3 4.5 4.5 4.4 4.4
0
1.2 2.1 2.2 2.4
[2] 1mb2.a 4.1 4.2 4.3 4.3 4.2 4.2 1.2
0
2.1 2.2 2.3
[2] 3fhj.a 4.1 4.1 4.3 4.3 4.2 4.2 2.1 2.1
0
2.5 2.9
[2] 3u1v.a 4.2 4.1 4.4 4.4 4.3 4.4 2.2 2.2 2.5
0
1.4
[2] 3u1v.d 3.8 3.8 3.9 3.9 3.9 3.9 2.4 2.3 2.9 1.4
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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