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SYA_ECOLI_2_442

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

Composition of the binding site

Protein chains monomer [domain annotation]
A1 (SYA_ECOLI):R: Catalytic (42, 44, 70, 77, 86:88, 91, 93, 171, 184, 210, 211, 213, 215, 236:240, 243)42, 44, 70, 77, 86:88, 91, 93, 171, 184, 210, 211, 213, 215, 236:240, 243

Full PDB list

3hxu, 3hxv, 3hxw, 3hxx, 3hxy, 3hxz, 3hy0, 3hy1

Pocket contact map

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PDB.ch
   
ligand
A1
A
4
2
M
4
4
R
7
0
D
7
7
R
8
6
H
8
7
H
8
8
F
9
1
M
9
3
W
1
7
1
E
1
8
4
E
2
1
0
I
2
1
1
N
2
1
3
V
2
1
5
D
2
3
6
T
2
3
7
G
2
3
8
G
2
4
0
R
2
4
3
[1]3hxu.a a5a28 . . . . . . . . . . . . . . . . . . . .
[1]3hxv.a g5a27 . . . . . . . . . . . . . . . . . . . .
[1]3hxw.a ssa29 . . . . . . . . . . . . . . . . . . . .
[1]3hxx.a acp,mg,mg,mg34 . . . . . . . . . . . . . . . . . . . .
[1]3hxy.a 5al,acp,mdn,mg,mg70 . . . . . . . . . . . . . . . . . . . .
[1]3hxz.a a5a28 . . . . . . . . . . . . . . . . . A . .
[1]3hy0.a g5a27 . . . . . . . . . . . . . . . . . A . .
[1]3hy1.a mg,ssa30 . . . . . . . . . . . . . . . . . A . .
[1]3hy1.b none . . . . . . . . . . . . . . . . . A . .

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
A
4
2
M
4
4
R
7
0
D
7
7
R
8
6
H
8
7
H
8
8
F
9
1
M
9
3
W
1
7
1
E
1
8
4
E
2
1
0
I
2
1
1
N
2
1
3
V
2
1
5
D
2
3
6
T
2
3
7
G
2
3
8
M
2
3
9
G
2
4
0
R
2
4
3
[1]3hxu.a . . . . . . . . . . . . . . . . . . . . .
[1]3hxv.a . . . . . . . . . . . . . . . . . . . . .
[1]3hxw.a . . . . . . . . . . . . . . . . . . . . .
[1]3hxx.a . . . . . . . . . * . . . . . . . . . . .
[1]3hxy.a . . . . . . . . . . . . . . . . . . . . .
[1]3hxz.a . . . . . . . . . . . . . . . . . A . . .
[1]3hy0.a . . . . . . . . . . . . . . . . . A . . .
[1]3hy1.a . . . . . . . . . . . . . . . . . A . . .
[1]3hy1.b . . . . . . . . . . . . . . . . . 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
3hxu.a:a5a
3hxv.a:g5a
3hxw.a:ssa
3hxx.a:acp,mg
3hxy.a:5al,acp,mdn,mg
3hxz.a:a5a
3hy0.a:g5a
3hy1.a:mg,ssa
3hy1.b is apo
[1] 3hxu.a
0.1
0 0 0.4 0.7 0 0 0.4 -
[1] 3hxv.a 0.1
0.1
0.1 0.5 1.0 0 0 0.5 -
[1] 3hxw.a 0.1 0
0
0.4 0.7 0 0.1 0.2 -
[1] 3hxx.a 1.1 1.1 1.2
0.2
1.3 1.2 1.1 1.9 -
[1] 3hxy.a 0.1 0 0.1 0.3
0.3
0 0 0.6 -
[1] 3hxz.a 0.1 0 0 0.3 0.7
0
0 0.4 -
[1] 3hy0.a 0.2 0.1 0.4 0.3 0.8 0.2
0.1
0.5 -
[1] 3hy1.a 0 0 0 0.2 0.1 0 0.1
0.4
-
[1] 3hy1.b 0.3 0.3 0.3 0.3 0.3 0.3 0.3 0.6
-
[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
3hxu.a
3hxv.a
3hxw.a
3hxx.a
3hxy.a
3hxz.a
3hy0.a
3hy1.a
3hy1.b
[1] 3hxu.a
0
.01 .01 .10 .04 .01 .03 .04 .04
[1] 3hxv.a .01
0
.03 .10 .03 .01 .03 .04 .05
[1] 3hxw.a .01 .03
0
.10 .04 .01 .03 .03 .03
[1] 3hxx.a .10 .10 .10
0
.08 .10 .10 .10 .10
[1] 3hxy.a .04 .03 .04 .08
0
.03 .04 .04 .05
[1] 3hxz.a .01 .01 .01 .10 .03
0
.02 .03 .04
[1] 3hy0.a .03 .03 .03 .10 .04 .02
0
.05 .04
[1] 3hy1.a .04 .04 .03 .10 .04 .03 .05
0
.04
[1] 3hy1.b .04 .05 .03 .10 .05 .04 .04 .04
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
3hxu.a
3hxv.a
3hxw.a
3hxx.a
3hxy.a
3hxz.a
3hy0.a
3hy1.a
3hy1.b
[1] 3hxu.a
0
0.1 0.1 0.4 0.3 0.1 0.1 0.3 1.0
[1] 3hxv.a 0.1
0
0.1 0.4 0.4 0.2 0.1 0.3 1.0
[1] 3hxw.a 0.1 0.1
0
0.4 0.4 0.1 0.1 0.3 1.0
[1] 3hxx.a 0.4 0.4 0.4
0
0.2 0.4 0.3 0.3 0.9
[1] 3hxy.a 0.3 0.4 0.4 0.2
0
0.4 0.3 0.4 0.9
[1] 3hxz.a 0.1 0.2 0.1 0.4 0.4
0
0.2 0.2 1.0
[1] 3hy0.a 0.1 0.1 0.1 0.3 0.3 0.2
0
0.3 1.0
[1] 3hy1.a 0.3 0.3 0.3 0.3 0.4 0.2 0.3
0
0.9
[1] 3hy1.b 1.0 1.0 1.0 0.9 0.9 1.0 1.0 0.9
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 0.3 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
3hxu.a
3hxv.a
3hxw.a
3hxx.a
3hxy.a
3hxz.a
3hy0.a
3hy1.a
3hy1.b
[1] 3hxu.a
0
0.1 0.1 0.5 0.4 0.2 0.2 0.5 1.8
[1] 3hxv.a 0.1
0
0.1 0.5 0.4 0.2 0.1 0.6 1.8
[1] 3hxw.a 0.1 0.1
0
0.5 0.4 0.2 0.2 0.5 1.8
[1] 3hxx.a 0.5 0.5 0.5
0
0.4 0.6 0.5 0.7 1.8
[1] 3hxy.a 0.4 0.4 0.4 0.4
0
0.4 0.4 0.6 1.7
[1] 3hxz.a 0.2 0.2 0.2 0.6 0.4
0
0.2 0.5 1.8
[1] 3hy0.a 0.2 0.1 0.2 0.5 0.4 0.2
0
0.6 1.8
[1] 3hy1.a 0.5 0.6 0.5 0.7 0.6 0.5 0.6
0
1.8
[1] 3hy1.b 1.8 1.8 1.8 1.8 1.7 1.8 1.8 1.8
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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