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SYM_THET8_1_501

Methionine--tRNA ligase [Class-I aminoacyl-tRNA synthetase family. MetG type 2A subfamily]

Composition of the binding site

Protein chains monomer
A1 (SYM_THET8):10, 11, 226, 227, 230, 231, 233, 234, 261, 264, 26510, 11, 226, 227, 230, 231, 233, 234, 261, 264, 265
Metals (Me):Zn

Full PDB list

1a8h, 1woy, 2d54, 2d5b, 3vu8 (redundant Pocketome entry)

Pocket contact map

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PDB.ch
   
ligand
A1 Me
P
1
0
I
1
1
V
2
2
6
W
2
2
7
A
2
3
0
N
2
3
3
Y
2
3
4
I
2
6
1
P
2
6
4
H
2
6
5
[1]1a8h.a none . . . . . . . . . . Zn
[1]3vu8.a mds10 . . . . . . . . . . Zn

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 Me
P
1
0
I
1
1
V
2
2
6
W
2
2
7
A
2
3
0
L
2
3
1
N
2
3
3
Y
2
3
4
I
2
6
1
P
2
6
4
H
2
6
5
[1]1a8h.a . . . . . . . . . . . Zn
[1]3vu8.a . . . . . . . . . . . Zn

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
1a8h.a is apo
3vu8.a:mds
[1] 1a8h.a
-
0
[1] 3vu8.a -
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
1a8h.a
3vu8.a
[1] 1a8h.a
0
0
[1] 3vu8.a 0
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 0.4 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
1a8h.a
3vu8.a
[1] 1a8h.a
0
0.2
[1] 3vu8.a 0.2
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 0.1 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
1a8h.a
3vu8.a
[1] 1a8h.a
0
0.7
[1] 3vu8.a 0.7
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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