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SYP_PLAF7_250_746

Proline--tRNA ligase [Class-II aminoacyl-tRNA synthetase family. ProS type 3 subfamily]

Composition of the binding site

Protein chains monomer
A1 (SYP_PLAF7):262, 263, 266, 276, 285, 287, 291, 396:404, 470, 474, 513, 514, 516:518, 520, 521, 707, 746262, 263, 266, 276, 285, 287, 291, 396:404, 470, 474, 513, 514, 516:518, 520, 521, 707, 746

Full PDB list

4ncx, 4olf, 4q15, 4twa, 4wi1, 4ydq, 5ifu (redundant Pocketome entry)

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1
F
2
6
2
S
2
6
3
Y
2
6
6
I
2
7
6
Y
2
8
5
L
2
8
7
A
2
9
1
R
4
0
3
E
4
0
4
N
4
7
0
I
4
7
4
T
5
1
3
R
5
1
4
I
5
1
6
G
5
1
7
I
5
1
8
I
5
2
0
M
5
2
1
Y
7
4
6
[1]4wi1.a 3o628 . . . . . . . . . . . . . . . . . . .
[1]5ifu.a gbm33 . . . . . . . . . . . . . . . . . . .
[2]4twa.a none . . . . . . . . . . . . . . . . . . .

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
F
2
6
2
S
2
6
3
Y
2
6
6
I
2
7
6
Y
2
8
5
L
2
8
7
A
2
9
1
P
3
9
6
T
3
9
7
P
3
9
8
F
3
9
9
I
4
0
0
R
4
0
1
T
4
0
2
R
4
0
3
E
4
0
4
N
4
7
0
I
4
7
4
T
5
1
3
R
5
1
4
I
5
1
6
G
5
1
7
I
5
1
8
I
5
2
0
M
5
2
1
L
7
0
7
Y
7
4
6
[1]4wi1.a . . . . . . . - - - - - - - . . . . . . . . . . . - .
[1]5ifu.a . . . . . . . - - - - - - . . . . . . . . . . . . . .
[2]4twa.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
4wi1.a:3o6
5ifu.a:gbm
4twa.a is apo
[1] 4wi1.a
0
0.9 -
[1] 5ifu.a 0.6
0
-
[2] 4twa.a 16 13
-
[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
4wi1.a
5ifu.a
4twa.a
[1] 4wi1.a
0
.04 .64
[1] 5ifu.a .04
0
.63
[2] 4twa.a .64 .63
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
4wi1.a
5ifu.a
4twa.a
[1] 4wi1.a
0
0.5 1.2
[1] 5ifu.a 0.5
0
1.2
[2] 4twa.a 1.2 1.2
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 0.5 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
4wi1.a
5ifu.a
4twa.a
[1] 4wi1.a
0
0.9 2.4
[1] 5ifu.a 0.9
0
1.7
[2] 4twa.a 2.4 1.7
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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