If you see this message after the page is completely loaded, then JavaScript is not supported or disabled in your browser. Please consider enabling JavaScript for this site.

AACL1_BRADU_2_326

Amino acid--[acyl-carrier-protein] ligase 1 [Class-II aminoacyl-tRNA synthetase family. Amino acid--[acyl-carrier-protein] ligase subfamily]

Composition of the binding site

Protein chains monomer
A1 (AACL1_BRADU):85, 88, 129, 131, 132, 159, 161, 167:169, 172, 174, 176, 215:217, 224, 225, 228, 229, 232, 234, 235, 237, 250:253, 255:258, 260, 261, 279, 281, 283, 285, 28685, 88, 129, 131, 132, 159, 161, 167:169, 172, 174, 176, 215:217, 224, 225, 228, 229, 232, 234, 235, 237, 250:253, 255:258, 260, 261, 279, 281, 283, 285, 286
Metals (Me):Zn

Full PDB list

3mey, 3mf1, 3mf2, 3pzc, 4h2s, 4h2t, 4h2u, 4h2v, 4h2w, 4h2x, 4h2y

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1 Me
F
8
5
A
1
2
9
C
1
3
1
Y
1
3
2
R
1
5
9
E
1
6
1
D
1
6
7
R
1
6
8
L
1
6
9
F
1
7
2
M
1
7
4
E
1
7
6
D
2
1
5
P
2
1
6
F
2
1
7
K
2
2
5
S
2
2
8
Q
2
2
9
Q
2
3
2
L
2
3
4
K
2
3
5
E
2
3
7
A
2
5
0
C
2
5
1
M
2
5
2
S
2
5
3
N
2
5
5
H
2
5
7
R
2
5
8
H
2
6
0
F
2
6
1
C
2
7
9
A
2
8
1
G
2
8
3
R
2
8
6
[1]3mey.a atp,mg32 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Zn
[1]3mf1.a g5a27 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Zn
[1]3mf2.a amp23 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Zn
[1]3pzc.a gap27 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Zn
[1]3pzc.b coa35 . . . . . . . . . . . . - - - - - - - . . . . . . . . . . . . . . . . Zn
[1]4h2s.b amp,pns,S50 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Zn
[1]4h2t.b g5a,pns,S54 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Zn
[1]4h2u.a atp,pns,S58 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Zn
[1]4h2u.b atp,mg,pns,S59 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Zn
[1]4h2v.a amp,h2v,S54 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Zn
[1]4h2w.a 5gp,pns,S51 . . . . . . . . . . . . . . . L N . . . . . . . . . . . . . . . . . . Zn
[1]4h2w.b amp,pns,S50 . . . . . . . . . . . . . . . L N . . . . . . . . . . . . . . . . . . Zn
[1]4h2x.a g5a,pns,S54 . . * . . . . . . . . . . . . L N . . . . . . . . . . . . . . * . . .
[1]4h2x.b g5a,pns,S54 . . . . . . . . . . . . . . . L N . . . . . . . . . . . . . . . . . . Zn
[1]4h2y.a atp,mg,pns,S59 . . . . . . . . . . . . . . . L N . . . . . . . . . . . . . . . . . . Zn
[1]4h2y.b atp,pns,S58 . . . . . . . . . . . . . . . L N . . . . . . . . . . . . . . . . . . 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

[download in TSV format]
   
PDB.ch
A1 Me
F
8
5
L
8
8
A
1
2
9
C
1
3
1
Y
1
3
2
R
1
5
9
E
1
6
1
D
1
6
7
R
1
6
8
L
1
6
9
F
1
7
2
M
1
7
4
E
1
7
6
D
2
1
5
P
2
1
6
F
2
1
7
M
2
2
4
K
2
2
5
S
2
2
8
Q
2
2
9
Q
2
3
2
L
2
3
4
K
2
3
5
E
2
3
7
A
2
5
0
C
2
5
1
M
2
5
2
S
2
5
3
N
2
5
5
Y
2
5
6
H
2
5
7
R
2
5
8
H
2
6
0
F
2
6
1
C
2
7
9
A
2
8
1
G
2
8
3
D
2
8
5
R
2
8
6
[1]3mey.a . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Zn
[1]3mf1.a . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Zn
[1]3mf2.a . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Zn
[1]3pzc.a . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Zn
[1]3pzc.b . . . . . . . . . . . . . - - - - - - - - . . . . . . . . . . * . . . . . . . Zn
[1]4h2s.b . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Zn
[1]4h2t.b . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Zn
[1]4h2u.a . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Zn
[1]4h2u.b . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Zn
[1]4h2v.a . . . . . . . . * . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Zn
[1]4h2w.a . . . . . * . . . . . . . . . . . L N . . . . . . . . . . . . . . . . . . . . Zn
[1]4h2w.b . . . . . . . . . . . . . . . . . L N . . . . . . . . . . . . . . . . . . . . Zn
[1]4h2x.a . . . * . . . . . . . . . . . . . L N . . . . . . . . . . . . . . . * . . . .
[1]4h2x.b . . . . . . . . * . . . . . . . . L N . . . . . . . . . . . . . . . . . . . . Zn
[1]4h2y.a . . . . . . . . . . . . . . . . . L N . . . . . . . . . . . . . . . . . . . . Zn
[1]4h2y.b . . . . . . . . * . . . . . . . . L N . . . . . . . . . . . . . . . . . . . . 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

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

pocketligand
≥10
9
8
7
6
5
4
3
2
1
0
3mey.a:atp,mg
3mf1.a:g5a
3mf2.a:amp
3pzc.a:gap
3pzc.b:coa
4h2s.b:S,amp,pns
4h2t.b:S,g5a,pns
4h2u.a:S,atp,pns
4h2u.b:S,atp,mg,pns
4h2v.a:S,amp,h2v
4h2w.a:5gp,S,pns
4h2w.b:S,amp,pns
4h2x.a:S,g5a,pns
4h2x.b:S,g5a,pns
4h2y.a:S,atp,mg,pns
4h2y.b:S,atp,pns
[1] 3mey.a
0
0 0 0 1.7 0.2 0 0.1 0.1 0.3 0.3 0.1 0 0.3 0.9 0.5
[1] 3mf1.a 0
0
0.1 0 1.3 0.1 0 0.2 0.2 0.1 0.2 0.2 0.1 0.1 0.4 0.3
[1] 3mf2.a 0 0
0
0 1.4 0.2 0 0.2 0.1 0.1 0.2 0 0.1 0.1 0.4 0.2
[1] 3pzc.a 0 0 0
0
1.1 0.1 0 0.1 0.1 0 0.1 0 0 0 0.2 0.1
[1] 3pzc.b 0.3 0.3 0.2 0.2
0.1
1.3 1.0 1.5 2.0 0.8 1.5 1.3 1.6 1.6 2.6 1.9
[1] 4h2s.b 0 0 0 0 0.9
0.1
0 0.1 0.1 0.1 0.2 0 0.1 0.1 0.4 0.3
[1] 4h2t.b 0 0 0 0 1.0 0.1
0
0.2 0.3 0.1 0.2 0.1 0.1 0.1 0.6 0.3
[1] 4h2u.a 0.1 0 0 0 1.7 0 0
0.1
0.2 0 0.2 0 0.1 0.1 0.7 0.3
[1] 4h2u.b 0 0 0 0 1.4 0 0 0.1
0.1
0.1 0.1 0 0.1 0.1 0.7 0.3
[1] 4h2v.a 0.1 0 0 0 1.9 0.1 0 0.1 0.2
0
0.1 0 0 0 0.9 0.2
[1] 4h2w.a 0.8 0.1 0.2 0.1 0.5 0.6 0.4 0.9 1.0 1.3
0.3
0.3 0.1 0.3 0.3 0.4
[1] 4h2w.b 0 0 0 0 1.4 0.5 0.1 0.6 0.2 0.9 0.2
0.1
0.1 0.1 0.4 0.3
[1] 4h2x.a 0.2 0.2 0.2 0.2 1.7 0.7 0.6 1.1 0.4 1.6 0.4 0.2
0.3
0.4 0.4 0.3
[1] 4h2x.b 0 0 0 0 1.8 0.5 0.1 0.5 0.2 1.1 0.2 0.1 0
0.1
0.5 0.1
[1] 4h2y.a 0.1 0 0 0 1.2 0.5 0.3 0.5 0.2 1.3 0 0 0 0
0.2
0.1
[1] 4h2y.b 0.1 0.1 0.1 0.1 1.6 0.5 0.2 0.5 0.3 1.0 0.1 0.1 0 0 0.8
0.2
[Pocket-ligand steric clashes matrix]

Pocket clash dissimilarity (1 cluster)

Pockets (x) vs pockets (y) colored by ligand clash profile difference

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

pocketpocket
≥1.
.9
.8
.7
.6
.5
.4
.3
.2
.1
.0
3mey.a
3mf1.a
3mf2.a
3pzc.a
3pzc.b
4h2s.b
4h2t.b
4h2u.a
4h2u.b
4h2v.a
4h2w.a
4h2w.b
4h2x.a
4h2x.b
4h2y.a
4h2y.b
[1] 3mey.a
0
.02 .02 .03 .11 .03 .03 .02 .02 .02 .06 .05 .06 .04 .06 .04
[1] 3mf1.a .02
0
.02 .01 .09 .01 .02 .02 .02 .02 .04 .04 .05 .04 .05 .05
[1] 3mf2.a .02 .02
0
.02 .11 .03 .02 .03 .03 .03 .05 .04 .06 .05 .05 .06
[1] 3pzc.a .03 .01 .02
0
.08 .01 .02 .03 .03 .03 .04 .05 .06 .05 .05 .05
[1] 3pzc.b .11 .09 .11 .08
0
.08 .09 .11 .10 .11 .11 .12 .14 .13 .13 .12
[1] 4h2s.b .03 .01 .03 .01 .08
0
.01 .04 .03 .03 .04 .05 .06 .05 .06 .05
[1] 4h2t.b .03 .02 .02 .02 .09 .01
0
.04 .03 .04 .04 .05 .06 .05 .06 .06
[1] 4h2u.a .02 .02 .03 .03 .11 .04 .04
0
.01 .01 .06 .04 .06 .04 .05 .03
[1] 4h2u.b .02 .02 .03 .03 .10 .03 .03 .01
0
.02 .05 .04 .06 .04 .05 .03
[1] 4h2v.a .02 .02 .03 .03 .11 .03 .04 .01 .02
0
.05 .05 .06 .03 .06 .03
[1] 4h2w.a .06 .04 .05 .04 .11 .04 .04 .06 .05 .05
0
.02 .03 .03 .03 .04
[1] 4h2w.b .05 .04 .04 .05 .12 .05 .05 .04 .04 .05 .02
0
.03 .02 .02 .02
[1] 4h2x.a .06 .05 .06 .06 .14 .06 .06 .06 .06 .06 .03 .03
0
.04 .03 .04
[1] 4h2x.b .04 .04 .05 .05 .13 .05 .05 .04 .04 .03 .03 .02 .04
0
.04 .02
[1] 4h2y.a .06 .05 .05 .05 .13 .06 .06 .05 .05 .06 .03 .02 .03 .04
0
.03
[1] 4h2y.b .04 .05 .06 .05 .12 .05 .06 .03 .03 .03 .04 .02 .04 .02 .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

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
3mey.a
3mf1.a
3mf2.a
3pzc.a
3pzc.b
4h2s.b
4h2t.b
4h2u.a
4h2u.b
4h2v.a
4h2w.a
4h2w.b
4h2x.a
4h2x.b
4h2y.a
4h2y.b
[1] 3mey.a
0
0.2 0.2 0.2 0.6 0.2 0.3 0.2 0.4 0.2 0.3 0.4 0.4 0.4 0.3 0.3
[1] 3mf1.a 0.2
0
0.2 0.1 0.6 0.2 0.3 0.2 0.4 0.2 0.4 0.4 0.5 0.5 0.4 0.4
[1] 3mf2.a 0.2 0.2
0
0.2 0.6 0.2 0.3 0.2 0.4 0.2 0.4 0.4 0.4 0.4 0.4 0.4
[1] 3pzc.a 0.2 0.1 0.2
0
0.6 0.2 0.3 0.2 0.4 0.2 0.4 0.4 0.4 0.4 0.4 0.4
[1] 3pzc.b 0.6 0.6 0.6 0.6
0
0.6 0.6 0.6 0.6 0.6 0.6 0.6 0.6 0.6 0.6 0.6
[1] 4h2s.b 0.2 0.2 0.2 0.2 0.6
0
0.1 0.1 0.3 0.2 0.3 0.3 0.3 0.3 0.3 0.3
[1] 4h2t.b 0.3 0.3 0.3 0.3 0.6 0.1
0
0.2 0.2 0.2 0.3 0.3 0.3 0.3 0.3 0.3
[1] 4h2u.a 0.2 0.2 0.2 0.2 0.6 0.1 0.2
0
0.3 0.1 0.3 0.3 0.3 0.3 0.3 0.3
[1] 4h2u.b 0.4 0.4 0.4 0.4 0.6 0.3 0.2 0.3
0
0.4 0.3 0.3 0.3 0.3 0.4 0.3
[1] 4h2v.a 0.2 0.2 0.2 0.2 0.6 0.2 0.2 0.1 0.4
0
0.4 0.4 0.4 0.4 0.4 0.4
[1] 4h2w.a 0.3 0.4 0.4 0.4 0.6 0.3 0.3 0.3 0.3 0.4
0
0.2 0.1 0.2 0.2 0.2
[1] 4h2w.b 0.4 0.4 0.4 0.4 0.6 0.3 0.3 0.3 0.3 0.4 0.2
0
0.2 0.1 0.3 0.1
[1] 4h2x.a 0.4 0.5 0.4 0.4 0.6 0.3 0.3 0.3 0.3 0.4 0.1 0.2
0
0.2 0.2 0.2
[1] 4h2x.b 0.4 0.5 0.4 0.4 0.6 0.3 0.3 0.3 0.3 0.4 0.2 0.1 0.2
0
0.2 0.1
[1] 4h2y.a 0.3 0.4 0.4 0.4 0.6 0.3 0.3 0.3 0.4 0.4 0.2 0.3 0.2 0.2
0
0.2
[1] 4h2y.b 0.3 0.4 0.4 0.4 0.6 0.3 0.3 0.3 0.3 0.4 0.2 0.1 0.2 0.1 0.2
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

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
3mey.a
3mf1.a
3mf2.a
3pzc.a
3pzc.b
4h2s.b
4h2t.b
4h2u.a
4h2u.b
4h2v.a
4h2w.a
4h2w.b
4h2x.a
4h2x.b
4h2y.a
4h2y.b
[1] 3mey.a
0
0.4 0.5 0.4 1.7 0.8 0.8 0.6 0.8 0.6 1.1 0.7 1.0 0.8 0.8 0.8
[1] 3mf1.a 0.4
0
0.3 0.3 1.6 0.8 0.8 0.7 0.9 0.7 1.1 0.8 1.0 0.8 0.9 0.8
[1] 3mf2.a 0.5 0.3
0
0.3 1.7 0.8 0.8 0.7 0.9 0.7 1.1 0.8 1.0 0.8 0.8 0.8
[1] 3pzc.a 0.4 0.3 0.3
0
1.7 0.8 0.8 0.6 0.8 0.6 1.1 0.7 0.9 0.7 0.8 0.7
[1] 3pzc.b 1.7 1.6 1.7 1.7
0
1.4 1.5 1.7 1.5 1.7 1.5 1.7 1.6 1.7 1.7 1.7
[1] 4h2s.b 0.8 0.8 0.8 0.8 1.4
0
0.4 0.6 0.5 0.6 1.1 0.8 0.9 0.8 0.8 0.9
[1] 4h2t.b 0.8 0.8 0.8 0.8 1.5 0.4
0
0.6 0.4 0.6 1.1 0.8 0.9 0.7 0.8 0.8
[1] 4h2u.a 0.6 0.7 0.7 0.6 1.7 0.6 0.6
0
0.6 0.3 1.0 0.6 0.8 0.6 0.7 0.6
[1] 4h2u.b 0.8 0.9 0.9 0.8 1.5 0.5 0.4 0.6
0
0.6 1.0 0.7 0.8 0.7 0.7 0.7
[1] 4h2v.a 0.6 0.7 0.7 0.6 1.7 0.6 0.6 0.3 0.6
0
1.1 0.7 0.9 0.7 0.8 0.7
[1] 4h2w.a 1.1 1.1 1.1 1.1 1.5 1.1 1.1 1.0 1.0 1.1
0
0.9 0.7 0.9 0.8 0.9
[1] 4h2w.b 0.7 0.8 0.8 0.7 1.7 0.8 0.8 0.6 0.7 0.7 0.9
0
0.7 0.1 0.5 0.4
[1] 4h2x.a 1.0 1.0 1.0 0.9 1.6 0.9 0.9 0.8 0.8 0.9 0.7 0.7
0
0.7 0.4 0.6
[1] 4h2x.b 0.8 0.8 0.8 0.7 1.7 0.8 0.7 0.6 0.7 0.7 0.9 0.1 0.7
0
0.6 0.4
[1] 4h2y.a 0.8 0.9 0.8 0.8 1.7 0.8 0.8 0.7 0.7 0.8 0.8 0.5 0.4 0.6
0
0.6
[1] 4h2y.b 0.8 0.8 0.8 0.7 1.7 0.9 0.8 0.6 0.7 0.7 0.9 0.4 0.6 0.4 0.6
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

L C X E | Background Color: | Anaglyph Stereo:

loading...