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GARS_HUMAN_114_739

Glycine--tRNA ligase [Class-II aminoacyl-tRNA synthetase family]

Composition of the binding site

Protein chains monomer [domain annotation]
A1 (GARS_HUMAN):R: Substrate binding (346, 348, 350)
R: Substrate binding (576, 578, 580)
194, 196:201, 213, 215, 216, 247, 248, 280, 281, 298, 299, 301, 331, 333, 340:343, 432, 435, 436, 440, 446, 457:460, 464, 583
194, 196:201, 213, 215, 216, 247, 248, 280, 281, 298, 299, 301, 331, 333, 340:343, 346, 348, 350, 432, 435, 436, 440, 446, 457:460, 464, 576, 578, 580, 583

Full PDB list

2pme, 2pmf, 2q5h, 2q5i, 2zt5, 2zt6, 2zt7, 2zt8, 2zxf, 4kqe, 4kr2, 4kr3, 4qei, 5e6m (redundant Pocketome entry)

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1
H
1
9
4
F
1
9
8
D
2
0
0
R
2
1
3
D
2
4
7
L
2
8
0
P
2
9
8
E
2
9
9
R
3
3
1
E
3
3
3
L
3
4
0
I
3
4
1
R
3
4
2
V
3
4
3
F
3
4
6
M
3
4
8
E
3
5
0
H
4
3
2
N
4
3
5
E
4
3
6
Y
4
4
0
E
4
5
7
I
4
5
8
V
4
5
9
R
4
6
4
E
5
7
6
S
5
7
8
G
5
8
0
R
5
8
3
[1]2zt5.a b4p53 . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]2zt6.a apc31 . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]2zt7.a atp,G36 . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]2zt8.a drv27 . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[2]4kqe.a none . . . . . . . . . . . . . . . . . . . . - . . . . . . . .
[2]4kr2.a amp23 . - - - - . . . . . . . . . . . . . - - - . . . . . . . .
[2]4kr3.a anp,G36 . . - - - . . . . . . . . . . . . . . - - . . . . . . . .
[2]5e6m.a CA,gap69 . . . - - . . . . . . . . . . . . . . . - . . . . . . . .
[3]2pmf.a none . . . . . . . . . . . . . . . . . . . - - . . . . . . R .

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
H
1
9
4
D
1
9
6
K
1
9
7
F
1
9
8
A
1
9
9
D
2
0
0
F
2
0
1
R
2
1
3
D
2
1
5
H
2
1
6
D
2
4
7
N
2
4
8
L
2
8
0
M
2
8
1
P
2
9
8
E
2
9
9
A
3
0
1
R
3
3
1
E
3
3
3
L
3
4
0
I
3
4
1
R
3
4
2
V
3
4
3
F
3
4
6
M
3
4
8
E
3
5
0
H
4
3
2
N
4
3
5
E
4
3
6
Y
4
4
0
D
4
4
6
E
4
5
7
I
4
5
8
V
4
5
9
G
4
6
0
R
4
6
4
E
5
7
6
S
5
7
8
G
5
8
0
R
5
8
3
[1]2zt5.a . . . * . * . * * . . . * . . . . . . . . * . . . . . . . . . . . . . . . . . .
[1]2zt6.a . . . * . * . * * . . . * . . . . . . . . . . . . . . . . * . . . . . . . . . .
[1]2zt7.a . . . * . * . * * . . . * . . . . . . . . * . . . . . . . . . . . . . * . . . .
[1]2zt8.a . . . * . * . * * . . . * . . . . . . . . . . . . . . . . * . . . . . * . . . .
[2]4kqe.a . . . * . . . * . . . . . . . . . * . . . . . . . . . . . - . . . . . . . . . .
[2]4kr2.a . . - - - - - - - - - - . . . . . . . . . . . . . . . - - - . . . . . . . . . .
[2]4kr3.a . . . . - - - - - - - - . . . . . . . . . . . . . . . . - - . . . . . . . . . .
[2]5e6m.a . . . . . . . - - - - - . . . . . . . . . . . . . . . . . - . . . . . . . . . .
[3]2pmf.a . . * * . . . * . . . . . . . . . . . . . . . . . . . . - - . . . . . . . . R .

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
2zt5.a:b4p
2zt6.a:apc
2zt7.a:G,atp
2zt8.a:drv
4kqe.a is apo
4kr2.a:amp
4kr3.a:G,anp
5e6m.a:CA,gap
2pmf.a is apo
[1] 2zt5.a
0.2
0.8 0.7 0.9 - 0.4 2.1 12 -
[1] 2zt6.a 0.2
0.4
0.5 0.5 - 0.3 2.0 11 -
[1] 2zt7.a 0.4 0.9
0.1
0.1 - 0.5 2.3 10 -
[1] 2zt8.a 0.9 1.2 0.6
0.2
- 0.5 2.3 11 -
[2] 4kqe.a 1.2 0.6 0.4 0.3
-
0.2 0.4 7.1 -
[2] 4kr2.a 0.1 0.1 0.4 0.2 -
0
0.1 0.5 -
[2] 4kr3.a 0.2 0.2 0.6 0.5 - 0.2
0
0.3 -
[2] 5e6m.a 0.1 0.3 0.5 0.6 - 0.2 0.5
0
-
[3] 2pmf.a 5.5 5.5 5.3 5.2 - 4.6 4.4 10
-
[Pocket-ligand steric clashes matrix]

Pocket clash dissimilarity (3 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
2zt5.a
2zt6.a
2zt7.a
2zt8.a
4kqe.a
4kr2.a
4kr3.a
5e6m.a
2pmf.a
[1] 2zt5.a
0
.07 .07 .09 .27 .37 .37 .36 .44
[1] 2zt6.a .07
0
.06 .07 .22 .32 .32 .31 .39
[1] 2zt7.a .07 .06
0
.06 .22 .33 .34 .33 .40
[1] 2zt8.a .09 .07 .06
0
.22 .33 .34 .33 .39
[2] 4kqe.a .27 .22 .22 .22
0
.19 .20 .20 .25
[2] 4kr2.a .37 .32 .33 .33 .19
0
.02 .04 .29
[2] 4kr3.a .37 .32 .34 .34 .20 .02
0
.03 .30
[2] 5e6m.a .36 .31 .33 .33 .20 .04 .03
0
.29
[3] 2pmf.a .44 .39 .40 .39 .25 .29 .30 .29
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 2.0 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
2zt5.a
2zt6.a
2zt7.a
2zt8.a
4kqe.a
4kr2.a
4kr3.a
5e6m.a
2pmf.a
[1] 2zt5.a
0
0.3 0.2 0.5 1.8 0.9 1.6 3.0 2.1
[1] 2zt6.a 0.3
0
0.3 0.5 1.6 0.8 1.5 2.9 2.0
[1] 2zt7.a 0.2 0.3
0
0.4 1.7 0.9 1.6 3.0 2.1
[1] 2zt8.a 0.5 0.5 0.4
0
1.6 0.9 1.6 2.9 1.9
[2] 4kqe.a 1.8 1.6 1.7 1.6
0
0.7 1.2 2.2 1.6
[2] 4kr2.a 0.9 0.8 0.9 0.9 0.7
0
0.6 0.5 1.3
[2] 4kr3.a 1.6 1.5 1.6 1.6 1.2 0.6
0
0.9 2.1
[2] 5e6m.a 3.0 2.9 3.0 2.9 2.2 0.5 0.9
0
2.9
[3] 2pmf.a 2.1 2.0 2.1 1.9 1.6 1.3 2.1 2.9
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 1.3 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
2zt5.a
2zt6.a
2zt7.a
2zt8.a
4kqe.a
4kr2.a
4kr3.a
5e6m.a
2pmf.a
[1] 2zt5.a
0
0.4 0.3 0.6 2.1 1.2 2.1 3.0 3.1
[1] 2zt6.a 0.4
0
0.4 0.6 2.0 1.2 2.0 2.9 3.0
[1] 2zt7.a 0.3 0.4
0
0.5 2.1 1.2 2.1 2.9 3.1
[1] 2zt8.a 0.6 0.6 0.5
0
2.0 1.3 2.1 2.9 3.0
[2] 4kqe.a 2.1 2.0 2.1 2.0
0
1.3 1.9 2.4 2.7
[2] 4kr2.a 1.2 1.2 1.2 1.3 1.3
0
1.0 0.9 2.3
[2] 4kr3.a 2.1 2.0 2.1 2.1 1.9 1.0
0
1.1 2.9
[2] 5e6m.a 3.0 2.9 2.9 2.9 2.4 0.9 1.1
0
3.1
[3] 2pmf.a 3.1 3.0 3.1 3.0 2.7 2.3 2.9 3.1
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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