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SYH_THET8_1_421

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

Composition of the binding site

Protein chains monomer [domain annotation]
A1 (SYH_THET8):R: Catalytic (81, 83, 112, 114, 119:121, 124, 126, 128, 130)
R: Catalytic (259, 261, 263, 264, 281:286, 288, 304:308, 311)
81, 83, 112, 114, 119:121, 124, 126, 128, 130, 259, 261, 263, 264, 281:286, 288, 304:308, 311

Full PDB list

1adj, 1ady, 1h4v, 4rdx

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1
E
8
1
T
8
3
R
1
1
2
E
1
1
4
G
1
1
9
R
1
2
0
Y
1
2
1
F
1
2
4
Q
1
2
6
E
1
3
0
R
2
5
9
L
2
6
1
Y
2
6
3
Y
2
6
4
A
2
8
1
L
2
8
2
G
2
8
3
G
2
8
4
G
2
8
5
G
2
8
6
Y
2
8
8
G
3
0
4
F
3
0
5
A
3
0
6
F
3
0
7
G
3
0
8
R
3
1
1
[1]1adj.c H11 . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]1ady.a ham33 . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]1h4v.b none . . . . - - . . . . . . . . . . . . . . . . . . . . .
[1]4rdx.a ampH34 . . . . . . . . . . . . . . . . . . . . . . . . . . .

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
E
8
1
T
8
3
R
1
1
2
E
1
1
4
G
1
1
9
R
1
2
0
Y
1
2
1
F
1
2
4
Q
1
2
6
N
1
2
8
E
1
3
0
R
2
5
9
L
2
6
1
Y
2
6
3
Y
2
6
4
A
2
8
1
L
2
8
2
G
2
8
3
G
2
8
4
G
2
8
5
G
2
8
6
Y
2
8
8
G
3
0
4
F
3
0
5
A
3
0
6
F
3
0
7
G
3
0
8
R
3
1
1
[1]1adj.c . . . . . . . . . . . * . . * . . . . . . . . . . . . .
[1]1ady.a . . . . . . . . . . . * . . * . . . . . . . . . . . . .
[1]1h4v.b . . * . - - . . . . . . . . . . . . . . . . . . . . . .
[1]4rdx.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
1adj.c:H
1ady.a:ham
1h4v.b is apo
4rdx.a:ampH
[1] 1adj.c
0.1
0.1 - 2.7
[1] 1ady.a 0.1
0.2
- 2.8
[1] 1h4v.b 0.1 2.5
-
2.0
[1] 4rdx.a 0.3 0.2 -
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
1adj.c
1ady.a
1h4v.b
4rdx.a
[1] 1adj.c
0
.01 .19 .11
[1] 1ady.a .01
0
.19 .12
[1] 1h4v.b .19 .19
0
.10
[1] 4rdx.a .11 .12 .10
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 1.7 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
1adj.c
1ady.a
1h4v.b
4rdx.a
[1] 1adj.c
0
1.4 1.6 1.9
[1] 1ady.a 1.4
0
1.6 1.1
[1] 1h4v.b 1.6 1.6
0
1.0
[1] 4rdx.a 1.9 1.1 1.0
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 1.2 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
1adj.c
1ady.a
1h4v.b
4rdx.a
[1] 1adj.c
0
1.7 2.1 2.4
[1] 1ady.a 1.7
0
2.2 1.7
[1] 1h4v.b 2.1 2.2
0
1.8
[1] 4rdx.a 2.4 1.7 1.8
0
[Binding site full-atom RMSD matrix]







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[ENTRY 2D visualization]

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