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ACACB_HUMAN_228_767

Acetyl-CoA carboxylase 2

Composition of the binding site

Protein chains monomer [domain annotation]
A1 (ACACB_HUMAN):D: Biotin carboxylation (270, 273, 274, 277, 278, 281, 351, 587, 590, 593, 594, 598, 599, 648, 671, 678:681, 683, 704:706)
D: ATP-grasp (587, 590, 593, 594, 598, 599)
234:237
234:237, 270, 273, 274, 277, 278, 281, 351, 587, 590, 593, 594, 598, 599, 648, 671, 678:681, 683, 704:706

Full PDB list

2hjw, 3gid, 3glk, 3jrw, 3jrx, 4hq6, 5kkn (redundant Pocketome entry)

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1
I
2
7
0
V
2
7
3
K
2
7
4
R
2
7
7
S
2
7
8
R
2
8
1
V
5
8
7
P
5
9
0
E
5
9
3
M
5
9
4
V
5
9
8
N
5
9
9
V
6
4
8
K
6
7
8
N
6
7
9
V
6
8
0
W
6
8
1
F
7
0
4
S
7
0
5
W
7
0
6
[1]3gid.a s1a37 . . . . . . . . . . . . . . . . . . . .
[1]3glk.a none . . . . . . . . . . . . . . . . . . . .
[1]5kkn.b 6u340 . . . . . . . . . . . . . . . . . . . .
[2]3jrw.a none . . . . . . . . . . . . . . . . . . . .

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
K
2
3
4
K
2
3
5
L
2
3
6
D
2
3
7
I
2
7
0
V
2
7
3
K
2
7
4
R
2
7
7
S
2
7
8
R
2
8
1
W
3
5
1
V
5
8
7
P
5
9
0
E
5
9
3
M
5
9
4
V
5
9
8
N
5
9
9
V
6
4
8
E
6
7
1
K
6
7
8
N
6
7
9
V
6
8
0
W
6
8
1
Y
6
8
3
F
7
0
4
S
7
0
5
W
7
0
6
[1]3gid.a - - - - . . . . . . . . . . . . . . . . . . . . . . .
[1]3glk.a - - - - . . . . . * . . . . . . . . . . . . * . . . .
[1]5kkn.b - - - - . . . . . * . . . . . . . . . . . . . . . . .
[2]3jrw.a S M sep G . . . . . . . . . . * . . . . . . . * . . . .

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
3gid.a:s1a
3glk.a is apo
5kkn.b:6u3
3jrw.a is apo
[1] 3gid.a
0
- 0.5 -
[1] 3glk.a 6.8
-
5.4 -
[1] 5kkn.b 1.7 -
0.1
-
[2] 3jrw.a 16 - 14
-
[Pocket-ligand steric clashes matrix]

Pocket clash dissimilarity (2 clusters)

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
3gid.a
3glk.a
5kkn.b
3jrw.a
[1] 3gid.a
0
.26 .08 .64
[1] 3glk.a .26
0
.21 .58
[1] 5kkn.b .08 .21
0
.72
[2] 3jrw.a .64 .58 .72
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 1.5 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
3gid.a
3glk.a
5kkn.b
3jrw.a
[1] 3gid.a
0
0.5 0.4 0.5
[1] 3glk.a 0.5
0
0.8 0.5
[1] 5kkn.b 0.4 0.8
0
0.7
[2] 3jrw.a 0.5 0.5 0.7
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 0.5 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
3gid.a
3glk.a
5kkn.b
3jrw.a
[1] 3gid.a
0
1.6 0.9 1.5
[1] 3glk.a 1.6
0
1.7 1.6
[1] 5kkn.b 0.9 1.7
0
1.6
[2] 3jrw.a 1.5 1.6 1.6
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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