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SYFA_THET8_85_350

Phenylalanine--tRNA ligase alpha subunit [Class-II aminoacyl-tRNA synthetase family. Phe-tRNA synthetase alpha subunit type 1 subfamily]

Composition of the binding site

Protein chains monomer
A1 (SYFA_THET8):148, 149, 178, 180, 183, 204, 206, 211:213, 216, 218, 220, 258, 260, 261, 280:284, 314:318, 320, 321, 332148, 149, 178, 180, 183, 204, 206, 211:213, 216, 218, 220, 258, 260, 261, 280:284, 314:318, 320, 321, 332
Metals (Me):Mg/Mn

Full PDB list

1b70, 1b7y, 1eiy, 1jjc, 1pys, 2akw, 2aly, 2amc, 2iy5, 3hfz, 3teh, 4tva (redundant Pocketome entry)

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1 Me
M
1
4
8
W
1
4
9
H
1
7
8
S
1
8
0
Q
1
8
3
R
2
0
4
E
2
0
6
H
2
1
2
E
2
1
3
F
2
1
6
Q
2
1
8
E
2
2
0
F
2
5
8
F
2
6
0
V
2
6
1
L
2
8
0
G
2
8
1
G
2
8
2
A
2
8
3
G
2
8
4
A
3
1
4
F
3
1
5
G
3
1
6
L
3
1
7
G
3
1
8
R
3
2
1
I
3
3
2
[1]1b70.a F12 . . . . . . . . . . . . . . . . . . . . . . . . . . . Mg
[1]1b7y.a fya33 . . . . . . . . . . . . . . . . . . . . . . . . . . . Mg
[1]1eiy.a A22 . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]1jjc.a fa534 . . . . . . . . . . . . . . . . . . . . . . . . . . . Mn
[1]1pys.a none . . . . . . . . . . . . . . . . . . . . . . . . . . . Mg
[1]2akw.a 20013 . . . . . . . . . . . . . . . . . . . . . . . . . . . Mn
[1]2aly.a ysa35 . . . . . . . . . . . . . . . . . . . . . . . . . . . Mn
[1]2amc.a Y13 . . . . . . . . . . . . . . . . . . . . . . . . . . . Mg
[1]3hfz.a mty13 . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]3teh.a dah14 . . . . . . . . . . . . . . . . . . . . . . . . . . .

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
M
1
4
8
W
1
4
9
H
1
7
8
S
1
8
0
Q
1
8
3
R
2
0
4
E
2
0
6
T
2
1
1
H
2
1
2
E
2
1
3
F
2
1
6
Q
2
1
8
E
2
2
0
F
2
5
8
F
2
6
0
V
2
6
1
L
2
8
0
G
2
8
1
G
2
8
2
A
2
8
3
G
2
8
4
A
3
1
4
F
3
1
5
G
3
1
6
L
3
1
7
G
3
1
8
E
3
2
0
R
3
2
1
I
3
3
2
[1]1b70.a . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Mg
[1]1b7y.a . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Mg
[1]1eiy.a . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]1jjc.a . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Mn
[1]1pys.a . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Mg
[1]2akw.a . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Mn
[1]2aly.a . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Mn
[1]2amc.a . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Mg
[1]3hfz.a . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]3teh.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

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pocketligand
≥10
9
8
7
6
5
4
3
2
1
0
1b70.a:F
1b7y.a:fya
1eiy.a:A
1jjc.a:fa5
1pys.a is apo
2akw.a:200
2aly.a:ysa
2amc.a:Y
3hfz.a:mty
3teh.a:dah
[1] 1b70.a
0
0.1 0.2 0.1 - 0.1 0 0.2 0.1 0.1
[1] 1b7y.a 0
0.1
0.2 0.1 - 0.3 0.1 0.2 0.1 0
[1] 1eiy.a 0.4 0.6
0.3
0.2 - 0.3 0.4 0.1 0 0.1
[1] 1jjc.a 0 0.1 0.4
0.2
- 0.4 0 0.1 0 0
[1] 1pys.a 0.3 0.1 0 0
-
0.1 0 0 0 0.1
[1] 2akw.a 0 0 0.1 0.1 -
0
0 0.1 0.1 0
[1] 2aly.a 0.1 0.1 0.2 0.3 - 0.3
0
0.1 0.1 0.1
[1] 2amc.a 0 0.1 0 0.2 - 0.3 0
0
0.1 0
[1] 3hfz.a 0.1 0 0.1 0.1 - 0.2 0 0
0
0
[1] 3teh.a 0 0.1 0.1 0.1 - 0.2 0.1 0 0
0.2
[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
1b70.a
1b7y.a
1eiy.a
1jjc.a
1pys.a
2akw.a
2aly.a
2amc.a
3hfz.a
3teh.a
[1] 1b70.a
0
.01 .04 .02 .02 .01 .02 .02 .02 .02
[1] 1b7y.a .01
0
.04 .02 .03 .02 .03 .02 .02 .03
[1] 1eiy.a .04 .04
0
.05 .04 .05 .06 .05 .04 .06
[1] 1jjc.a .02 .02 .05
0
.04 .03 .02 .02 .03 .02
[1] 1pys.a .02 .03 .04 .04
0
.02 .03 .03 .02 .02
[1] 2akw.a .01 .02 .05 .03 .02
0
.03 .02 .02 .02
[1] 2aly.a .02 .03 .06 .02 .03 .03
0
.02 .03 .02
[1] 2amc.a .02 .02 .05 .02 .03 .02 .02
0
.01 .02
[1] 3hfz.a .02 .02 .04 .03 .02 .02 .03 .01
0
.03
[1] 3teh.a .02 .03 .06 .02 .02 .02 .02 .02 .03
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
1b70.a
1b7y.a
1eiy.a
1jjc.a
1pys.a
2akw.a
2aly.a
2amc.a
3hfz.a
3teh.a
[1] 1b70.a
0
0.4 0.5 0.4 0.4 0.3 0.6 0.3 0.4 0.4
[1] 1b7y.a 0.4
0
0.6 0.6 0.7 0.6 0.4 0.6 0.6 0.5
[1] 1eiy.a 0.5 0.6
0
0.6 0.5 0.5 0.7 0.5 0.5 0.5
[1] 1jjc.a 0.4 0.6 0.6
0
0.6 0.3 0.6 0.3 0.3 0.3
[1] 1pys.a 0.4 0.7 0.5 0.6
0
0.4 0.8 0.4 0.5 0.5
[1] 2akw.a 0.3 0.6 0.5 0.3 0.4
0
0.7 0.2 0.3 0.3
[1] 2aly.a 0.6 0.4 0.7 0.6 0.8 0.7
0
0.7 0.7 0.7
[1] 2amc.a 0.3 0.6 0.5 0.3 0.4 0.2 0.7
0
0.3 0.3
[1] 3hfz.a 0.4 0.6 0.5 0.3 0.5 0.3 0.7 0.3
0
0.3
[1] 3teh.a 0.4 0.5 0.5 0.3 0.5 0.3 0.7 0.3 0.3
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
1b70.a
1b7y.a
1eiy.a
1jjc.a
1pys.a
2akw.a
2aly.a
2amc.a
3hfz.a
3teh.a
[1] 1b70.a
0
0.9 1.2 0.7 0.9 0.9 0.9 0.9 0.9 0.9
[1] 1b7y.a 0.9
0
1.3 1.0 1.3 1.1 0.7 1.2 1.2 1.1
[1] 1eiy.a 1.2 1.3
0
1.3 0.9 1.0 1.4 1.0 1.0 1.0
[1] 1jjc.a 0.7 1.0 1.3
0
1.0 0.8 0.9 0.9 0.9 0.9
[1] 1pys.a 0.9 1.3 0.9 1.0
0
0.5 1.1 0.5 0.5 0.7
[1] 2akw.a 0.9 1.1 1.0 0.8 0.5
0
1.0 0.3 0.5 0.5
[1] 2aly.a 0.9 0.7 1.4 0.9 1.1 1.0
0
1.1 1.1 1.0
[1] 2amc.a 0.9 1.2 1.0 0.9 0.5 0.3 1.1
0
0.4 0.6
[1] 3hfz.a 0.9 1.2 1.0 0.9 0.5 0.5 1.1 0.4
0
0.6
[1] 3teh.a 0.9 1.1 1.0 0.9 0.7 0.5 1.0 0.6 0.6
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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