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SYH_ECOLI_1_424

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

Composition of the binding site

Protein chains monomer
A1 (SYH_ECOLI):83:85, 107, 113, 115, 120:122, 125, 127, 131, 259, 261, 263, 264, 281, 282, 284:286, 288, 304:306, 308, 31183:85, 107, 113, 115, 120:122, 125, 127, 131, 259, 261, 263, 264, 281, 282, 284:286, 288, 304:306, 308, 311

Full PDB list

1htt, 1kmm, 1kmn, 2el9

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1
E
8
3
T
8
5
R
1
1
3
E
1
1
5
G
1
2
0
R
1
2
1
Y
1
2
2
F
1
2
5
Q
1
2
7
E
1
3
1
R
2
5
9
L
2
6
1
Y
2
6
3
Y
2
6
4
T
2
8
1
V
2
8
2
A
2
8
4
G
2
8
5
Y
2
8
8
G
3
0
4
F
3
0
5
A
3
0
6
G
3
0
8
R
3
1
1
[1]1htt.b Hamp33 . . . . . . . . . . . . . . . . . . . . . . . .
[1]1kmm.a ham33 . . . . . . . . . . . . . . . . . . . . . . . .
[1]1kmn.c atp,hso41 . . . . . . . . . . . . . . . . . . . . . . . .
[1]2el9.a hss33 . . . . . . . . . . . . . . . . . . . . . . . .

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
E
8
3
G
8
4
T
8
5
Y
1
0
7
R
1
1
3
E
1
1
5
G
1
2
0
R
1
2
1
Y
1
2
2
F
1
2
5
Q
1
2
7
E
1
3
1
R
2
5
9
L
2
6
1
Y
2
6
3
Y
2
6
4
T
2
8
1
V
2
8
2
A
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
G
3
0
8
R
3
1
1
[1]1htt.b . . . . . . . * . . . . . . . . . . . . . . . . . . .
[1]1kmm.a . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]1kmn.c . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]2el9.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
1htt.b:Hamp
1kmm.a:ham
1kmn.c:atp,hso
2el9.a:hss
[1] 1htt.b
0.1
0.3 1.7 0.1
[1] 1kmm.a 0.1
0.1
0.4 0.3
[1] 1kmn.c 0.3 0.5
0.4
0.6
[1] 2el9.a 0.2 0.7 0.7
0.3
[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
1htt.b
1kmm.a
1kmn.c
2el9.a
[1] 1htt.b
0
.07 .06 .09
[1] 1kmm.a .07
0
.02 .03
[1] 1kmn.c .06 .02
0
.03
[1] 2el9.a .09 .03 .03
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 0.8 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
1htt.b
1kmm.a
1kmn.c
2el9.a
[1] 1htt.b
0
0.4 0.4 0.4
[1] 1kmm.a 0.4
0
0.4 0.4
[1] 1kmn.c 0.4 0.4
0
0.4
[1] 2el9.a 0.4 0.4 0.4
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 0.4 Å)

Pockets (x) vs pockets (y) colored by RMSD of all site residue atoms

zoom: [−] [+]; [view as image]; [download as text]

pocketpocket
≥10 Å
9 Å
8 Å
7 Å
6 Å
5 Å
4 Å
3 Å
2 Å
1 Å
0 Å
1htt.b
1kmm.a
1kmn.c
2el9.a
[1] 1htt.b
0
1.2 1.2 1.2
[1] 1kmm.a 1.2
0
0.8 0.5
[1] 1kmn.c 1.2 0.8
0
0.8
[1] 2el9.a 1.2 0.5 0.8
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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