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SYFA_PSEAE_1_338

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_PSEAE):143, 151, 171, 174, 175, 178, 195, 208, 210, 212, 248:251, 282, 283, 286, 290, 305:309143, 151, 171, 174, 175, 178, 195, 208, 210, 212, 248:251, 282, 283, 286, 290, 305:309

Full PDB list

4p71, 4p72, 4p73, 4p74, 4p75

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1
L
1
4
3
A
1
5
1
S
1
7
1
Q
1
7
4
M
1
7
8
Q
2
0
8
E
2
1
0
L
2
1
2
F
2
4
8
P
2
4
9
F
2
5
0
T
2
5
1
G
2
8
2
C
2
8
3
V
2
8
6
V
2
9
0
A
3
0
5
F
3
0
6
G
3
0
7
M
3
0
8
G
3
0
9
[1]4p71.c none . . . . . . . . . . . . . . . . . . . . .
[1]4p72.c 2nl20 . . . . . . . . . . . . . . . . . . . . .
[1]4p73.c gax30 . . . . . . . . . . . . . . . . . . . . .
[1]4p74.c 2u924 . . . . . . . . . . . . . . . . . . . . .
[1]4p75.c 2nm17 . . . . . . . . . . . . . . . . . . . . .

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
L
1
4
3
A
1
5
1
S
1
7
1
Q
1
7
4
V
1
7
5
M
1
7
8
R
1
9
5
Q
2
0
8
E
2
1
0
L
2
1
2
F
2
4
8
P
2
4
9
F
2
5
0
T
2
5
1
G
2
8
2
C
2
8
3
V
2
8
6
V
2
9
0
A
3
0
5
F
3
0
6
G
3
0
7
M
3
0
8
G
3
0
9
[1]4p71.c . . . . . . . . . . . . . . . . . . . . . . .
[1]4p72.c . . . . . . . . . . . . . . . . . . . . . . .
[1]4p73.c . . . . . . . . . . . . . . . . . . . . . . .
[1]4p74.c . . . . . . . . . . . . . . . . . . . . . . .
[1]4p75.c . . . . . . . . . . . . . . . . . . . . . . .

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
4p71.c is apo
4p72.c:2nl
4p73.c:gax
4p74.c:2u9
4p75.c:2nm
[1] 4p71.c
-
0.5 0.8 0.9 0.7
[1] 4p72.c -
0
0.2 0.2 0.1
[1] 4p73.c - 0
0
0.1 0.1
[1] 4p74.c - 0 0.4
0
0
[1] 4p75.c - 0 0.4 0
0
[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
4p71.c
4p72.c
4p73.c
4p74.c
4p75.c
[1] 4p71.c
0
.04 .05 .06 .06
[1] 4p72.c .04
0
.01 .02 .02
[1] 4p73.c .05 .01
0
.03 .03
[1] 4p74.c .06 .02 .03
0
0
[1] 4p75.c .06 .02 .03 0
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 0.5 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
4p71.c
4p72.c
4p73.c
4p74.c
4p75.c
[1] 4p71.c
0
0.3 0.3 0.2 0.2
[1] 4p72.c 0.3
0
0.2 0.1 0.1
[1] 4p73.c 0.3 0.2
0
0.2 0.2
[1] 4p74.c 0.2 0.1 0.2
0
0.1
[1] 4p75.c 0.2 0.1 0.2 0.1
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 0.2 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
4p71.c
4p72.c
4p73.c
4p74.c
4p75.c
[1] 4p71.c
0
1.1 0.5 1.0 1.1
[1] 4p72.c 1.1
0
1.0 0.2 0.2
[1] 4p73.c 0.5 1.0
0
1.0 1.0
[1] 4p74.c 1.0 0.2 1.0
0
0.1
[1] 4p75.c 1.1 0.2 1.0 0.1
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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