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AMDA_BORBO_1_240

Arylmalonate decarboxylase

Composition of the binding site

Protein chains monomer
A1 (AMDA_BORBO):14:17, 20, 43, 74:76, 104, 126, 156, 159, 188:19014:17, 20, 43, 74:76, 104, 126, 156, 159, 188:190

Full PDB list

2vlb, 3dg9, 3dtv, 3eis, 3ip8, 3ixl, 3ixm (redundant Pocketome entry)

Pocket contact map

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PDB.ch
   
ligand
A1
P
1
4
P
1
5
G
7
4
T
7
5
S
7
6
Y
1
2
6
V
1
5
6
M
1
5
9
C
1
8
8
G
1
8
9
G
1
9
0
[1]2vlb.c none . . . . . . . . . . .
[1]3dg9.a none . . . . . . . . . . .
[1]3eis.d none . . . . . . . . * . .
[1]3ip8.a b8511 . . . . . . . . . . .
[1]3ixl.a pac10 . . C . . . . . S . .
[1]3ixm.a none . . C . . . . . . . .

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
P
1
4
P
1
5
A
1
6
A
1
7
V
2
0
V
4
3
G
7
4
T
7
5
S
7
6
M
1
0
4
Y
1
2
6
V
1
5
6
M
1
5
9
C
1
8
8
G
1
8
9
G
1
9
0
[1]2vlb.c . . . * . . . . . . . . . . . .
[1]3dg9.a . . . . . . . . . . . . . . . .
[1]3eis.d . . . * . . . . . . . . . * . .
[1]3ip8.a . . . . . . . . . . . . . . . .
[1]3ixl.a . . . . . . C . . . . . . S . .
[1]3ixm.a . . . . . . C . . . . . . . . .

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
2vlb.c is apo
3dg9.a is apo
3eis.d is apo
3ip8.a:b85
3ixl.a:pac
3ixm.a is apo
[1] 2vlb.c
-
- - 2.8 2.0 -
[1] 3dg9.a -
-
- 0.2 0.1 -
[1] 3eis.d - -
-
3.4 2.5 -
[1] 3ip8.a - - -
0.1
0 -
[1] 3ixl.a - - - 0.4
0
-
[1] 3ixm.a - - - 0.6 0.2
-
[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
2vlb.c
3dg9.a
3eis.d
3ip8.a
3ixl.a
3ixm.a
[1] 2vlb.c
0
.17 .04 .17 .16 .16
[1] 3dg9.a .17
0
.20 .01 .02 .03
[1] 3eis.d .04 .20
0
.21 .19 .19
[1] 3ip8.a .17 .01 .21
0
.02 .03
[1] 3ixl.a .16 .02 .19 .02
0
.01
[1] 3ixm.a .16 .03 .19 .03 .01
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 4.8 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
2vlb.c
3dg9.a
3eis.d
3ip8.a
3ixl.a
3ixm.a
[1] 2vlb.c
0
5.9 0.5 5.9 5.8 5.0
[1] 3dg9.a 5.9
0
5.9 0.1 0.7 3.9
[1] 3eis.d 0.5 5.9
0
5.9 5.8 5.1
[1] 3ip8.a 5.9 0.1 5.9
0
0.7 3.9
[1] 3ixl.a 5.8 0.7 5.8 0.7
0
3.4
[1] 3ixm.a 5.0 3.9 5.1 3.9 3.4
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 3.9 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
2vlb.c
3dg9.a
3eis.d
3ip8.a
3ixl.a
3ixm.a
[1] 2vlb.c
0
6.7 0.6 6.7 6.5 5.3
[1] 3dg9.a 6.7
0
6.6 0.1 1.0 4.8
[1] 3eis.d 0.6 6.6
0
6.6 6.4 5.3
[1] 3ip8.a 6.7 0.1 6.6
0
1.0 4.8
[1] 3ixl.a 6.5 1.0 6.4 1.0
0
4.2
[1] 3ixm.a 5.3 4.8 5.3 4.8 4.2
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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