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ACS2A_HUMAN_30_577

Acyl-coenzyme A synthetase ACSM2A, mitochondrial [ATP-dependent AMP-binding enzyme family]

Composition of the binding site

Protein chains monomer
A1 (ACS2A_HUMAN):221:225, 229, 265:267, 270, 271, 337:340, 359:364, 367, 368, 383, 444, 446, 458, 461, 465:468, 472, 473, 538, 539, 552:557221:225, 229, 265:267, 270, 271, 337:340, 359:364, 367, 368, 383, 444, 446, 458, 461, 465:473, 538, 539, 552:557

Full PDB list

2vze, 2wd9, 3b7w, 3c5e, 3day, 3eq6, 3gpc (redundant Pocketome entry)

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1
T
2
2
1
S
2
2
2
G
2
2
3
T
2
2
4
S
2
2
5
K
2
2
9
W
2
6
5
I
2
6
6
L
2
6
7
L
2
7
0
V
3
3
7
G
3
3
8
E
3
3
9
S
3
4
0
E
3
5
9
S
3
6
0
Y
3
6
1
G
3
6
2
Q
3
6
3
T
3
6
4
L
3
6
8
M
3
8
3
D
4
4
6
F
4
5
8
R
4
6
1
N
4
6
7
G
4
7
0
R
4
7
2
T
5
5
5
K
5
5
7
[1]2wd9.a ibp15 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]3b7w.a none . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]3c5e.a atp,mg,unl,unl,unl,unl36 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]3day.a apc,mg32 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]3eq6.b amp23 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]3gpc.b coa39 . . - - - . . . . . . . . . . . . . . . . . . . . . . . . .

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
T
2
2
1
S
2
2
2
G
2
2
3
T
2
2
4
S
2
2
5
K
2
2
9
W
2
6
5
I
2
6
6
L
2
6
7
L
2
7
0
C
2
7
1
V
3
3
7
G
3
3
8
E
3
3
9
S
3
4
0
E
3
5
9
S
3
6
0
Y
3
6
1
G
3
6
2
Q
3
6
3
T
3
6
4
G
3
6
7
L
3
6
8
M
3
8
3
L
4
4
4
D
4
4
6
F
4
5
8
R
4
6
1
I
4
6
5
I
4
6
6
N
4
6
7
S
4
6
8
S
4
6
9
G
4
7
0
Y
4
7
1
R
4
7
2
I
4
7
3
Y
5
3
8
K
5
3
9
K
5
5
2
T
5
5
3
V
5
5
4
T
5
5
5
G
5
5
6
K
5
5
7
[1]2wd9.a . * . . . . . . . . . . . . . . . . . . . . . . . . . . * . . . . * * * . . . . . . . . .
[1]3b7w.a . * . . . . . . . . . . . . . . . . . . . . . . . . . . * . . . . * . * . . . . . . . . .
[1]3c5e.a . * . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]3day.a . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]3eq6.b . * . . . . . . . . . . . . . . . . . . . . * . . . . . . . . . . * * * . . . . . . . . .
[1]3gpc.b . * - - - . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

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
2wd9.a:ibp
3b7w.a is apo
3c5e.a:atp,mg,unl
3day.a:apc,mg
3eq6.b:amp
3gpc.b:coa
[1] 2wd9.a
0
- 5.0 4.9 0.1 4.9
[1] 3b7w.a 0
-
6.0 5.8 0.1 5.7
[1] 3c5e.a 0 -
0
0.2 0 1.5
[1] 3day.a 0 - 0.1
0
0 1.8
[1] 3eq6.b 0.6 - 5.2 5.4
0
3.8
[1] 3gpc.b 0 - 1.5 1.9 0
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
2wd9.a
3b7w.a
3c5e.a
3day.a
3eq6.b
3gpc.b
[1] 2wd9.a
0
.04 .17 .20 .05 .17
[1] 3b7w.a .04
0
.19 .22 .07 .18
[1] 3c5e.a .17 .19
0
.04 .18 .03
[1] 3day.a .20 .22 .04
0
.22 .07
[1] 3eq6.b .05 .07 .18 .22
0
.15
[1] 3gpc.b .17 .18 .03 .07 .15
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 8.9 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
2wd9.a
3b7w.a
3c5e.a
3day.a
3eq6.b
3gpc.b
[1] 2wd9.a
0
1.3 16 16 1.1 16
[1] 3b7w.a 1.3
0
16 16 0.6 16
[1] 3c5e.a 16 16
0
0.3 16 1.1
[1] 3day.a 16 16 0.3
0
16 1.1
[1] 3eq6.b 1.1 0.6 16 16
0
16
[1] 3gpc.b 16 16 1.1 1.1 16
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 8.6 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
2wd9.a
3b7w.a
3c5e.a
3day.a
3eq6.b
3gpc.b
[1] 2wd9.a
0
1.3 17 17 1.3 17
[1] 3b7w.a 1.3
0
16 16 1.0 16
[1] 3c5e.a 17 16
0
1.0 16 1.1
[1] 3day.a 17 16 1.0
0
16 1.5
[1] 3eq6.b 1.3 1.0 16 16
0
16
[1] 3gpc.b 17 16 1.1 1.5 16
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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